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Gene: PIGY (phosphatidylinositol glycan anchor biosynthesis class Y) Homo sapiens

Analyze

Symbol:

PIGY

Name:

phosphatidylinositol glycan anchor biosynthesis class Y

RGD ID:

1605909

HGNC Page

HGNC:28213

Description:

Contributes to phosphatidylinositol N-acetylglucosaminyltransferase activity. Acts upstream of or within GPI anchor biosynthetic process. Located in endoplasmic reticulum membrane and plasma membrane. Part of glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex. Implicated in hyperphosphatasia with impaired intellectual development syndrome 6.

Type:

protein-coding

RefSeq Status:

REVIEWED

Previously known as:

HPMRS6; MGC14156; phosphatidylinositol glycan anchor biosynthesis, class Y; phosphatidylinositol glycan, class Y; phosphatidylinositol N-acetylglucosaminyltransferase subunit Y; phosphatidylinositol-glycan biosynthesis class Y protein; PIG-Y; PREY; protein preY, mitochondrial

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Related Pseudogenes:

LOC442064

Allele / Splice:

See ClinVar data

Latest Assembly:

GRCh38 - Human Genome Assembly GRCh38

Position:

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	4	88,520,998 - 88,523,776 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	4	88,520,998 - 88,523,776 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	4	89,442,149 - 89,444,927 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	89,661,158 - 89,663,978 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	4	86,738,822 - 86,741,642 (-)	NCBI		Celera
Cytogenetic Map	4	q22.1	NCBI
HuRef	4	85,194,129 - 85,196,952 (-)	NCBI		HuRef
CHM1_1	4	89,418,607 - 89,421,430 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	4	91,852,644 - 91,855,421 (-)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autosomal dominant polycystic kidney disease (IAGP)

hyperphosphatasia with impaired intellectual development syndrome (EXP)

hyperphosphatasia with impaired intellectual development syndrome 6 (IAGP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (ISO)

17alpha-ethynylestradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2-hydroxypropanoic acid (EXP)

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

6-propyl-2-thiouracil (ISO)

acetamide (ISO)

amitrole (ISO)

arsenite(3-) (EXP)

benzo[a]pyrene (EXP)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (ISO)

cadmium atom (EXP)

cadmium dichloride (EXP)

CGP 52608 (EXP)

chloropicrin (EXP)

chlorpyrifos (ISO)

choline (ISO)

cobalt dichloride (ISO)

copper(II) sulfate (EXP)

dibutyl phthalate (ISO)

finasteride (ISO)

flutamide (ISO)

folic acid (ISO)

gold atom (EXP)

gold(0) (EXP)

L-methionine (ISO)

methimazole (ISO)

Monobutylphthalate (ISO)

p-toluidine (ISO)

paracetamol (ISO)

perfluorooctane-1-sulfonic acid (EXP)

perfluorooctanoic acid (EXP)

phenobarbital (ISO)

pirinixic acid (ISO)

rac-lactic acid (EXP)

sodium arsenate (ISO)

sulfadimethoxine (ISO)

sulindac (ISO)

tamoxifen (ISO)

tetrachloromethane (ISO)

titanium dioxide (ISO)

valproic acid (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

GPI anchor biosynthetic process (IBA,IDA,IEA)

Cellular Component

endoplasmic reticulum (IEA)

endoplasmic reticulum membrane (IDA,IEA,TAS)

glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (IBA,IDA,IPI)

membrane (IEA)

plasma membrane (IDA)

Molecular Function

phosphatidylinositol N-acetylglucosaminyltransferase activity (IDA)

protein binding (IPI)

Molecular Pathway Annotations Click to see Annotation Detail View

glycosylphosphatidylinositol anchor biosynthetic pathway (IEA)

Phenotype Annotations Click to see Annotation Detail View

Human Phenotype

2-3 toe syndactyly (IAGP)

Abdominal pain (IAGP)

Abnormal facial shape (IAGP)

Abnormal parietal bone morphology (IAGP)

Abnormal renal collecting system morphology (IAGP)

Adducted thumb (IAGP)

Aganglionic megacolon (IAGP)

Aggressive behavior (IAGP)

Anteriorly placed anus (IAGP)

Anteverted nares (IAGP)

Ataxia (IAGP)

Autistic behavior (IAGP)

Autosomal recessive inheritance (IAGP)

Axial hypotonia (IAGP)

Bifid uvula (IAGP)

Bilateral tonic-clonic seizure (IAGP)

Brachycephaly (IAGP)

Broad philtrum (IAGP)

Bulbous nose (IAGP)

Cerebral hypomyelination (IAGP)

Cerebral visual impairment (IAGP)

Chronic lung disease (IAGP)

Clinodactyly (IAGP)

Clinodactyly of the 5th finger (IAGP)

Coarse facial features (IAGP)

Congenital onset (IAGP)

Cupped ear (IAGP)

Death in childhood (IAGP)

Death in infancy (IAGP)

Decreased head circumference (IAGP)

Deeply set eye (IAGP)

Depressed nasal bridge (IAGP)

Developmental cataract (IAGP)

Developmental regression (IAGP)

Downturned corners of mouth (IAGP)

Echogenic fetal bowel (IAGP)

EEG with multifocal slow activity (IAGP)

EEG with polyspike wave complexes (IAGP)

EEG with spike-wave complexes (IAGP)

Elbow flexion contracture (IAGP)

Elevated circulating alkaline phosphatase concentration (IAGP)

Elevated circulating creatine kinase concentration (IAGP)

Epicanthus (IAGP)

Esotropia (IAGP)

Feeding difficulties (IAGP)

Gait disturbance (IAGP)

Gastrostomy tube feeding in infancy (IAGP)

Global developmental delay (IAGP)

Growth delay (IAGP)

High palate (IAGP)

Highly arched eyebrow (IAGP)

Hip contracture (IAGP)

Hip dysplasia (IAGP)

Hydronephrosis (IAGP)

Hyperechogenic kidneys (IAGP)

Hypermetropia (IAGP)

Hypertelorism (IAGP)

Increased head circumference (IAGP)

Infantile muscular hypotonia (IAGP)

Inguinal hernia (IAGP)

Intellectual disability (IAGP)

Intellectual disability, moderate (IAGP)

Intellectual disability, severe (IAGP)

Knee flexion contracture (IAGP)

Large earlobe (IAGP)

Limb undergrowth (IAGP)

Long palpebral fissure (IAGP)

Mandibular prognathia (IAGP)

Micrognathia (IAGP)

Myoclonus (IAGP)

Narrow forehead (IAGP)

Necrotizing enterocolitis (IAGP)

Oculomotor apraxia (IAGP)

Oligohydramnios (IAGP)

Osteopenia (IAGP)

Pectus excavatum (IAGP)

Plagiocephaly (IAGP)

Polyhydramnios (IAGP)

Prominent nasal bridge (IAGP)

Reduced tendon reflexes (IAGP)

Round face (IAGP)

Scoliosis (IAGP)

Seizure (IAGP)

Shallow anterior chamber (IAGP)

Short neck (IAGP)

Short philtrum (IAGP)

Shortening of all distal phalanges of the fingers (IAGP)

Single umbilical artery (IAGP)

Small nail (IAGP)

Supernumerary nipple (IAGP)

Telangiectasia (IAGP)

Tented upper lip vermilion (IAGP)

Thickened ears (IAGP)

Thickened helices (IAGP)

Toe syndactyly (IAGP)

Upslanted palpebral fissure (IAGP)

Visual impairment (IAGP)

Vomiting (IAGP)

Wide nasal bridge (IAGP)

References

References - curated

#	Reference Title	Reference Citation
1.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
2.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:15489334	PMID:16162815	PMID:18187620	PMID:19302917	PMID:20877624	PMID:21873635	PMID:21988832	PMID:22925353	PMID:26293662	PMID:27503909	PMID:32296183
PMID:33961781

Genomics

Comparative Map Data

PIGY
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	4	88,520,998 - 88,523,776 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	4	88,520,998 - 88,523,776 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	4	89,442,149 - 89,444,927 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	89,661,158 - 89,663,978 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	4	86,738,822 - 86,741,642 (-)	NCBI		Celera
Cytogenetic Map	4	q22.1	NCBI
HuRef	4	85,194,129 - 85,196,952 (-)	NCBI		HuRef
CHM1_1	4	89,418,607 - 89,421,430 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	4	91,852,644 - 91,855,421 (-)	NCBI		T2T-CHM13v2.0

Pigyl
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	22,068,142 - 22,069,651 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	9	22,068,142 - 22,069,654 (+)	Ensembl		GRCm39 Ensembl
GRCm38	9	22,156,846 - 22,158,355 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	22,156,846 - 22,158,358 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	9	21,961,290 - 21,962,799 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	9	21,907,268 - 21,908,750 (+)	NCBI		MGSCv36	mm8
Celera	9	19,425,815 - 19,427,324 (+)	NCBI		Celera
Cytogenetic Map	9	A3	NCBI
cM Map	9	8.46	NCBI

Pigy
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	8	28,965,634 - 28,967,876 (+)	NCBI		GRCr8
mRatBN7.2	8	20,689,621 - 20,691,863 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	8	20,689,502 - 20,692,585 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	8	24,718,077 - 24,720,311 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	8	23,015,228 - 23,017,462 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	8	20,919,167 - 20,921,408 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	8	23,167,974 - 23,170,215 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	23,167,974 - 23,170,209 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	8	23,221,295 - 23,223,536 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	8	22,078,318 - 22,080,559 (+)	NCBI		Celera
Cytogenetic Map	8	q13	NCBI

Pigy
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955474	11,944,302 - 11,947,092 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955474	11,945,871 - 11,946,419 (+)	NCBI	ChiLan1.0	ChiLan1.0

LOC103784916
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	3	86,524,595 - 86,527,866 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	4	86,787,084 - 86,790,339 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	4	80,810,555 - 80,813,329 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	4	91,533,268 - 91,536,090 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	4	91,533,268 - 91,536,850 (-)	Ensembl	panpan1.1		panPan2

PIGY
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	32	11,808,967 - 11,812,436 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	32	30,142,083 - 30,145,550 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	32	11,862,485 - 11,865,733 (-)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	32	11,945,115 - 11,953,351 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	32	11,770,336 - 11,773,803 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	32	28,143,350 - 28,146,819 (+)	NCBI		UU_Cfam_GSD_1.0

Pigy
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405301	29,570,615 - 29,571,337 (+)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936685	984,606 - 985,106 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LOC110256448
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	13	162,392,377 - 162,394,317 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

PIGY
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	7	36,882,467 - 36,885,287 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	7	36,882,372 - 36,885,186 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	15,633,646 - 15,636,466 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Pigy
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624757	16,159,263 - 16,159,777 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in PIGY
15 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 4q12-22.3(chr4:51831622-97505618)x3	copy number gain	See cases [RCV000051772]	Chr4:51831622..97505618 [GRCh38] Chr4:52697788..98426769 [GRCh37] Chr4:52392545..98645792 [NCBI36] Chr4:4q12-22.3	pathogenic
GRCh38/hg38 4q13.3-22.1(chr4:74031395-90421127)x1	copy number loss	Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053296]\|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053296]\|See cases [RCV000053296]	Chr4:74031395..90421127 [GRCh38] Chr4:74897112..91342278 [GRCh37] Chr4:75115976..91561301 [NCBI36] Chr4:4q13.3-22.1	pathogenic
GRCh38/hg38 4q21.21-22.1(chr4:79575748-92412449)x1	copy number loss	See cases [RCV000053297]	Chr4:79575748..92412449 [GRCh38] Chr4:80496902..93333600 [GRCh37] Chr4:80715926..93552623 [NCBI36] Chr4:4q21.21-22.1	pathogenic
GRCh38/hg38 4q21.21-22.3(chr4:80879777-94809447)x1	copy number loss	See cases [RCV000134977]	Chr4:80879777..94809447 [GRCh38] Chr4:81800931..95730598 [GRCh37] Chr4:82019955..95949621 [NCBI36] Chr4:4q21.21-22.3	pathogenic
GRCh38/hg38 4q21.21-24(chr4:80427023-100855441)x1	copy number loss	See cases [RCV000137269]	Chr4:80427023..100855441 [GRCh38] Chr4:81348177..101776598 [GRCh37] Chr4:81567201..101995621 [NCBI36] Chr4:4q21.21-24	pathogenic
GRCh38/hg38 4q21.23-22.2(chr4:84329551-93654474)x1	copy number loss	See cases [RCV000139231]	Chr4:84329551..93654474 [GRCh38] Chr4:85250704..94575625 [GRCh37] Chr4:85469728..94794648 [NCBI36] Chr4:4q21.23-22.2	likely benign
GRCh38/hg38 4q21.23-22.2(chr4:85449365-93973194)x1	copy number loss	See cases [RCV000141424]	Chr4:85449365..93973194 [GRCh38] Chr4:86370518..94894345 [GRCh37] Chr4:86589542..95113368 [NCBI36] Chr4:4q21.23-22.2	pathogenic
GRCh38/hg38 4q13.2-22.3(chr4:68686088-95294456)x3	copy number gain	See cases [RCV000143458]	Chr4:68686088..95294456 [GRCh38] Chr4:69551806..96215607 [GRCh37] Chr4:69234401..96434630 [NCBI36] Chr4:4q13.2-22.3	pathogenic
NM_001042616.2(PIGY):c.-540G>A	single nucleotide variant	Hyperphosphatasia with intellectual disability syndrome 6 [RCV000207473]	Chr4:88523797 [GRCh38] Chr4:89444948 [GRCh37] Chr4:4q22.1	pathogenic
NM_001042616.3(PIGY):c.137T>C (p.Leu46Pro)	single nucleotide variant	Hyperphosphatasia with intellectual disability syndrome 6 [RCV000207478]	Chr4:88521653 [GRCh38] Chr4:89442804 [GRCh37] Chr4:4q22.1	pathogenic\|likely benign
NM_001042616.3(PIGY):c.17C>G (p.Pro6Arg)	single nucleotide variant	not provided [RCV000487837]	Chr4:88521773 [GRCh38] Chr4:89442924 [GRCh37] Chr4:4q22.1	likely benign\|conflicting interpretations of pathogenicity\|uncertain significance
GRCh37/hg19 4q21.23-22.1(chr4:85839771-93071150)x1	copy number loss	See cases [RCV000446648]	Chr4:85839771..93071150 [GRCh37] Chr4:4q21.23-22.1	pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:12440-190904441)x3	copy number gain	See cases [RCV000446653]	Chr4:12440..190904441 [GRCh37] Chr4:4p16.3-q35.2	pathogenic
GRCh37/hg19 4q21.23-24(chr4:85805268-103678797)x1	copy number loss	See cases [RCV000445741]	Chr4:85805268..103678797 [GRCh37] Chr4:4q21.23-24	pathogenic
GRCh37/hg19 4q21.21-22.1(chr4:82283358-90341831)x1	copy number loss	See cases [RCV000447691]	Chr4:82283358..90341831 [GRCh37] Chr4:4q21.21-22.1	pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:68346-190957473)	copy number gain	See cases [RCV000510453]	Chr4:68346..190957473 [GRCh37] Chr4:4p16.3-q35.2	pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:68346-190957473)x3	copy number gain	See cases [RCV000512241]	Chr4:68346..190957473 [GRCh37] Chr4:4p16.3-q35.2	pathogenic
GRCh37/hg19 4q21.21-22.3(chr4:81314915-96636651)x1	copy number loss	not provided [RCV000682426]	Chr4:81314915..96636651 [GRCh37] Chr4:4q21.21-22.3	pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:49450-190915650)x3	copy number gain	not provided [RCV000743155]	Chr4:49450..190915650 [GRCh37] Chr4:4p16.3-q35.2	pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:49450-190963766)x3	copy number gain	not provided [RCV000743156]	Chr4:49450..190963766 [GRCh37] Chr4:4p16.3-q35.2	pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:11525-191028879)x3	copy number gain	not provided [RCV000743147]	Chr4:11525..191028879 [GRCh37] Chr4:4p16.3-q35.2	pathogenic
NM_001042616.3(PIGY):c.143C>T (p.Pro48Leu)	single nucleotide variant	not provided [RCV000975043]	Chr4:88521647 [GRCh38] Chr4:89442798 [GRCh37] Chr4:4q22.1	likely benign
GRCh37/hg19 4q21.21-22.1(chr4:80482400-92572499)x1	copy number loss	See cases [RCV000790579]	Chr4:80482400..92572499 [GRCh37] Chr4:4q21.21-22.1	pathogenic
NM_001042616.3(PIGY):c.-222C>T	single nucleotide variant	not provided [RCV001691793]	Chr4:88522011 [GRCh38] Chr4:89443162 [GRCh37] Chr4:4q22.1	benign
Single allele	deletion	Autosomal dominant polycystic kidney disease [RCV001254217]	Chr4:88075149..90714489 [GRCh37] Chr4:4q22.1	pathogenic
GRCh38/hg38 4q22.1(chr4:88504598-90127832)x3	copy number gain	Autosomal dominant Parkinson disease 4 [RCV000015046]	Chr4:88504598..90127832 [GRCh38] Chr4:4q22.1	pathogenic
NM_032906.5(PYURF):c.289_290dup (p.Gln97fs)	microsatellite	Mitochondrial disease [RCV001537634]	Chr4:88521942..88521943 [GRCh38] Chr4:89443093..89443094 [GRCh37] Chr4:4q22.1	pathogenic
NM_001042616.3(PIGY):c.101G>A (p.Cys34Tyr)	single nucleotide variant	Hyperphosphatasia with intellectual disability syndrome 6 [RCV001335596]	Chr4:88521689 [GRCh38] Chr4:89442840 [GRCh37] Chr4:4q22.1	uncertain significance
NM_001042616.3(PIGY):c.-334C>T	single nucleotide variant	Hyperphosphatasia with intellectual disability syndrome 6 [RCV001335597]	Chr4:88523591 [GRCh38] Chr4:89444742 [GRCh37] Chr4:4q22.1	uncertain significance
NM_001042616.3(PIGY):c.151A>G (p.Ile51Val)	single nucleotide variant	Hyperphosphatasia with intellectual disability syndrome 6 [RCV001332724]\|not provided [RCV001865767]	Chr4:88521639 [GRCh38] Chr4:89442790 [GRCh37] Chr4:4q22.1	uncertain significance
NC_000004.12:g.88523885C>T	single nucleotide variant	not provided [RCV001716538]	Chr4:88523885 [GRCh38] Chr4:89445036 [GRCh37] Chr4:4q22.1	benign
NC_000004.12:g.88523787C>T	single nucleotide variant	not provided [RCV001775496]	Chr4:88523787 [GRCh38] Chr4:89444938 [GRCh37] Chr4:4q22.1	benign
GRCh37/hg19 4q21.21-22.1(chr4:80467886-93362064)x1	copy number loss	not provided [RCV001829208]	Chr4:80467886..93362064 [GRCh37] Chr4:4q21.21-22.1	pathogenic
GRCh37/hg19 4q13.3-22.1(chr4:75737340-91131156)	copy number gain	not specified [RCV002053429]	Chr4:75737340..91131156 [GRCh37] Chr4:4q13.3-22.1	pathogenic
GRCh37/hg19 4q21.21-22.1(chr4:81054789-90667421)	copy number loss	not specified [RCV002053435]	Chr4:81054789..90667421 [GRCh37] Chr4:4q21.21-22.1	pathogenic
GRCh37/hg19 4q12-31.21(chr4:52866944-143582507)x3	copy number gain	not provided [RCV001827738]	Chr4:52866944..143582507 [GRCh37] Chr4:4q12-31.21	pathogenic
GRCh37/hg19 4q21.21-22.2(chr4:79780152-94873225)	copy number loss	not specified [RCV002053432]	Chr4:79780152..94873225 [GRCh37] Chr4:4q21.21-22.2	pathogenic
GRCh37/hg19 4q21.23-22.1(chr4:85839771-93071150)	copy number loss	not specified [RCV002053440]	Chr4:85839771..93071150 [GRCh37] Chr4:4q21.23-22.1	pathogenic
NM_001042616.3(PIGY):c.110C>G (p.Thr37Arg)	single nucleotide variant	not provided [RCV001974170]	Chr4:88521680 [GRCh38] Chr4:89442831 [GRCh37] Chr4:4q22.1	uncertain significance
NM_001042616.3(PIGY):c.1A>G (p.Met1Val)	single nucleotide variant	not provided [RCV002012757]	Chr4:88521789 [GRCh38] Chr4:89442940 [GRCh37] Chr4:4q22.1	uncertain significance
NM_032906.5(PYURF):c.113A>C (p.Asp38Ala)	single nucleotide variant	not specified [RCV004210651]	Chr4:88523588 [GRCh38] Chr4:89444739 [GRCh37] Chr4:4q22.1	uncertain significance
NM_001042616.3(PIGY):c.16C>T (p.Pro6Ser)	single nucleotide variant	not provided [RCV002824569]	Chr4:88521774 [GRCh38] Chr4:89442925 [GRCh37] Chr4:4q22.1	uncertain significance
GRCh38/hg38 4q21.21-23(chr4:79123548-99457773)x1	copy number loss	Chromosome 4q21 deletion syndrome [RCV003327709]	Chr4:79123548..99457773 [GRCh38] Chr4:4q21.21-23	pathogenic
NM_001042616.3(PIGY):c.162T>C (p.Tyr54=)	single nucleotide variant	not provided [RCV003435099]	Chr4:88521628 [GRCh38] Chr4:89442779 [GRCh37] Chr4:4q22.1	likely benign
NM_001042616.3(PIGY):c.108C>G (p.Ser36Arg)	single nucleotide variant	not provided [RCV003838473]	Chr4:88521682 [GRCh38] Chr4:89442833 [GRCh37] Chr4:4q22.1	uncertain significance
NM_001042616.3(PIGY):c.46T>C (p.Ser16Pro)	single nucleotide variant	not provided [RCV003554429]	Chr4:88521744 [GRCh38] Chr4:89442895 [GRCh37] Chr4:4q22.1	uncertain significance
NM_001042616.3(PIGY):c.21G>A (p.Thr7=)	single nucleotide variant	not provided [RCV003820823]	Chr4:88521769 [GRCh38] Chr4:89442920 [GRCh37] Chr4:4q22.1	likely benign
GRCh37/hg19 4q21.23-22.3(chr4:85139670-96295033)x3	copy number gain	not specified [RCV003986489]	Chr4:85139670..96295033 [GRCh37] Chr4:4q21.23-22.3	likely pathogenic
GRCh37/hg19 4q21.21-22.3(chr4:81558759-95965995)x1	copy number loss	not specified [RCV003986493]	Chr4:81558759..95965995 [GRCh37] Chr4:4q21.21-22.3	pathogenic
GRCh37/hg19 4p12-q35.2(chr4:45455621-191003541)x3	copy number gain	not provided [RCV003885507]	Chr4:45455621..191003541 [GRCh37] Chr4:4p12-q35.2	pathogenic
NM_001042616.3(PIGY):c.20C>T (p.Thr7Met)	single nucleotide variant	not provided [RCV005197409]	Chr4:88521770 [GRCh38] Chr4:89442921 [GRCh37] Chr4:4q22.1	uncertain significance
NM_001042616.3(PIGY):c.107G>C (p.Ser36Thr)	single nucleotide variant	not provided [RCV005180700]	Chr4:88521683 [GRCh38] Chr4:89442834 [GRCh37] Chr4:4q22.1	uncertain significance

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	70
Count of miRNA genes:	70
Interacting mature miRNAs:	70
Transcripts:	ENST00000527353
Prediction methods:	Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region

SHGC-59828

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	4	89,442,288 - 89,442,410	UniSTS	GRCh37
Build 36	4	89,661,311 - 89,661,433	RGD	NCBI36
Celera	4	86,738,975 - 86,739,097	RGD
Cytogenetic Map	4	q	UniSTS
Cytogenetic Map	4	q22.1	UniSTS
HuRef	4	85,194,288 - 85,194,410	UniSTS
GeneMap99-GB4 RH Map	4	457.82	UniSTS
NCBI RH Map	4	1059.3	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Sequence

Nucleotide Sequences


RefSeq Transcripts	NG_046719	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_001042616	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB206972	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC083829	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC007876	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BI548853	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068274	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DB519150	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENST00000527353 ⟹ ENSP00000432688

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	4	88,520,998 - 88,523,776 (-)	Ensembl

RefSeq Acc Id:

NM_001042616 ⟹ NP_001036081

RefSeq Status:

REVIEWED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	4	88,520,998 - 88,523,776 (-)	NCBI
GRCh37	4	89,442,129 - 89,444,952 (-)	NCBI
Build 36	4	89,661,158 - 89,663,978 (-)	NCBI Archive
Celera	4	86,738,822 - 86,741,642 (-)	RGD
HuRef	4	85,194,129 - 85,196,952 (-)	NCBI
CHM1_1	4	89,418,607 - 89,421,430 (-)	NCBI
T2T-CHM13v2.0	4	91,852,644 - 91,855,421 (-)	NCBI

Sequence:

show sequence

CTGGACGAACGGGAAGCCGGGAGCTCGGCCACGGGTGGCGAGGCTGCGGTGAGGCCTGGTCTCC
GGCTGCCAGACCATGCTGAGTGGAGCACGCTGCAGGCTCGCCTCAGCGCTGCGGGGAACGCGCG
CGCCGCCGTCCGCGGTCGCCCGTAGGTGCCTGCACGCGTCGGGGTCGCGGCCTTTGGCCGACCG
GGGCAAGAAGACTGAGGAGCCGCCCCGCGACTTCGATCCGGCGCTGCTGGAGTTCCTGGTGTGC
CCGCTCTCCAAGAAGCCGCTCAGATATGAAGCATCAACAAACGAATTGATTAATGAAGAGTTGG
GAATAGCTTATCCAATCATTGATGGGATCCCTAATATGATACCACAGGCAGCTAGGATGACACG
TCAAAGTAAGAAGCAAGAAGAAGTGGAGCAGCGCTAGTTCATAATTTAAAAAAATTAAAAAAAC
GCAACAGCCAACTTTTCTTAATACCATATACCTTTTAAAACACAGTGGCAGGTAATAAGTGGAA
GAGAAGAATGTTTCTGTCTCTTCCTACGTTGACTGTTCTTATTCCACTGGTTTCTTTAGCAGGA
CTGTTCTACTCAGCCTCTGTGGAAGAAAACTTCCCACAGGGCTGCACTAGCACAGCCAGCCTTT
GCTTTTACAGCCTGCTCTTGCCTATTACCATACCAGTGTATGTATTCTTCCACCTTTGGACTTG
GATGGGTATTAAACTCTTCAGGCATAATTGATGCAACTAGAGTCAATATGCTGTATATATTAAT
GATAGCTCTTGGGCATCGATCTCTGAAAGCTCAAATGGATGGAATTTAGTTTGCGGGAAAGAGG
CTTTGCTTTGCGCATATCAGGCTTAGGACTGTGGGAGGCTTAAGTTGCAGATGCTTCTTTTATT
GTACTCTTGTTCTGCCCTTGTTTTTTGAAGGCTCTGACTTATAACTGCTGTATCAGAAGAAACA
TTTTGACAGTGTCTTGGTTGGAGATGAACATCCCTAATTGACATGTGATGACTATTTCTTATTC
CATTCATCTAAGAGTCATTGAAATTTTGTTTTGCTTGTTTGTTTAGCTTCAAGGTCTTTGGTAA
AGTCACATGTTAAGGATGACTGAAATAATTCCAAAGGAGTGATGTTGGAATAGTCCCTCTAAGG
GAGAGAAATGCATTTGAACGAATGTGATATAAAACCACATAATCAAATAGAAACTTCATGTACT
TACAAAAACTGAGTTTGTAAAATTACCTTCATTTCTTTGACATTAAATGCTTATATTAGCAATA
AACATGTTGACACTTTCCTATAAAAAATAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001036081	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH07876	(Get FASTA)	NCBI Sequence Viewer
	BAE44507	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSP00000432688
	ENSP00000432688.1
GenBank Protein	Q3MUY2	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_001036081 ⟸ NM_001042616
- UniProtKB:	Q3MUY2 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MFLSLPTLTVLIPLVSLAGLFYSASVEENFPQGCTSTASLCFYSLLLPITIPVYVFFHLWTWMG IKLFRHN hide sequence

Ensembl Acc Id:

ENSP00000432688 ⟸ ENST00000527353

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q3MUY2-F1-model_v2	AlphaFold	Q3MUY2	1-71	view protein structure

Promoters

RGD ID:

6802526

Promoter ID:

HG_KWN:48713

Type:

CpG-Island

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

CD4+TCell, CD4+TCell_12Hour, HeLa_S3, K562, Lymphoblastoid, NB4

Transcripts:

OTTHUMT00000253550

Position:

Human Assembly	Chr	Position (strand)	Source
Build 36	4	89,663,679 - 89,664,179 (-)	MPROMDB

RGD ID:

6850478

Promoter ID:

EP73030

Type:

initiation region

Name:

HS_MGC14156

Description:

Hypothetical protein MGC14156.

SO ACC ID:

SO:0000170

Source:

EPD (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

NEDO full length human cDNA sequencing project.; Oligo-capping

Position:

Human Assembly	Chr	Position (strand)	Source
Build 36	4	89,663,937 - 89,663,997	EPD

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	HGNC:28213	AgrOrtholog
COSMIC	PIGY	COSMIC
Ensembl Genes	ENSG00000255072	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENST00000527353	ENTREZGENE
	ENST00000527353.2	UniProtKB/Swiss-Prot
GTEx	ENSG00000255072	GTEx
HGNC ID	HGNC:28213	ENTREZGENE
Human Proteome Map	PIGY	Human Proteome Map
InterPro	PIG-Y	UniProtKB/Swiss-Prot
KEGG Report	hsa:84992	UniProtKB/Swiss-Prot
NCBI Gene	84992	ENTREZGENE
OMIM	610662	OMIM
PANTHER	PHOSPHATIDYLINOSITOL N-ACETYLGLUCOSAMINYLTRANSFERASE SUBUNIT Y	UniProtKB/Swiss-Prot
	PHOSPHATIDYLINOSITOL N-ACETYLGLUCOSAMINYLTRANSFERASE SUBUNIT Y	UniProtKB/Swiss-Prot
Pfam	PIG-Y	UniProtKB/Swiss-Prot
PharmGKB	PA143485576	PharmGKB
UniProt	PIGY_HUMAN	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-11-10	PIGY	phosphatidylinositol glycan anchor biosynthesis class Y		phosphatidylinositol glycan anchor biosynthesis, class Y	Symbol and/or name change	5135510	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

Imported Human Phenotype Annotations - HPO

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

Imported Human Phenotype Annotations - HPO