SCGB1D4 (secretoglobin family 1D member 4) - Rat Genome Database

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Gene: SCGB1D4 (secretoglobin family 1D member 4) Homo sapiens
Analyze
Symbol: SCGB1D4
Name: secretoglobin family 1D member 4
RGD ID: 1606365
HGNC Page HGNC:31748
Description: Predicted to be located in extracellular region. Predicted to be active in extracellular space.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: IFN-gamma inducible SCGB (IIS); IFN-gamma-inducible secretoglobin; IIS; secretoglobin, family 1D, member 4
RGD Orthologs
Rat
Bonobo
Dog
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Related Pseudogenes: SCGB1D5P  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381162,296,281 - 62,299,075 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1162,296,281 - 62,299,075 (-)EnsemblGRCh38hg38GRCh38
GRCh371162,063,753 - 62,066,547 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361161,820,330 - 61,823,112 (-)NCBINCBI36Build 36hg18NCBI36
Celera1159,393,130 - 59,395,911 (-)NCBICelera
Cytogenetic Map11q12.3NCBI
HuRef1158,392,136 - 58,394,918 (-)NCBIHuRef
CHM1_11161,946,974 - 61,949,756 (-)NCBICHM1_1
T2T-CHM13v2.01162,285,567 - 62,288,360 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:12975309   PMID:15034037   PMID:15340161   PMID:21873635   PMID:22155607   PMID:28263490   PMID:28514442   PMID:33961781  


Genomics

Comparative Map Data
SCGB1D4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381162,296,281 - 62,299,075 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1162,296,281 - 62,299,075 (-)EnsemblGRCh38hg38GRCh38
GRCh371162,063,753 - 62,066,547 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361161,820,330 - 61,823,112 (-)NCBINCBI36Build 36hg18NCBI36
Celera1159,393,130 - 59,395,911 (-)NCBICelera
Cytogenetic Map11q12.3NCBI
HuRef1158,392,136 - 58,394,918 (-)NCBIHuRef
CHM1_11161,946,974 - 61,949,756 (-)NCBICHM1_1
T2T-CHM13v2.01162,285,567 - 62,288,360 (-)NCBIT2T-CHM13v2.0
Scgb1d4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81215,755,363 - 215,758,238 (+)NCBIGRCr8
mRatBN7.21206,330,454 - 206,333,329 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1206,330,454 - 206,333,329 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1214,712,716 - 214,715,593 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01221,764,021 - 221,766,896 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01214,459,027 - 214,461,902 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01225,690,756 - 225,693,631 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1225,690,756 - 225,693,631 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01232,643,521 - 232,646,396 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41212,121,766 - 212,124,641 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11212,280,195 - 212,283,071 (+)NCBI
Celera1203,831,891 - 203,834,734 (+)NCBICelera
Cytogenetic Map1q43NCBI
SCGB1D4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2963,527,666 - 63,531,667 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11164,570,450 - 64,574,418 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01157,658,053 - 57,662,047 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11161,015,794 - 61,018,604 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1161,015,927 - 61,018,550 (-)Ensemblpanpan1.1panPan2
LOC100687441
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11854,335,333 - 54,338,102 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1852,905,523 - 52,908,291 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01855,388,974 - 55,391,740 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11854,450,899 - 54,453,643 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01854,058,681 - 54,061,449 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01854,923,474 - 54,926,248 (+)NCBIUU_Cfam_GSD_1.0
SCGB1D1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl29,387,355 - 9,391,370 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.129,387,546 - 9,391,171 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.228,709,589 - 8,713,214 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCGB1D4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1111,575,621 - 11,579,494 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666038108,931,299 - 108,934,217 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in SCGB1D4
5 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11q12.3(chr11:62249520-62946093)x3 copy number gain See cases [RCV000138411] Chr11:62249520..62946093 [GRCh38]
Chr11:62016992..62713565 [GRCh37]
Chr11:61773568..62470141 [NCBI36]
Chr11:11q12.3		 pathogenic
GRCh37/hg19 11q12.3(chr11:62039313-62063841)x3 copy number gain See cases [RCV000447153] Chr11:62039313..62063841 [GRCh37]
Chr11:11q12.3		 likely benign
GRCh37/hg19 11q12.3(chr11:61840997-62987330)x1 copy number loss See cases [RCV000448355] Chr11:61840997..62987330 [GRCh37]
Chr11:11q12.3		 likely pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470) copy number gain See cases [RCV000511729] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470)x3 copy number gain See cases [RCV000510881] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11q12.1-12.3(chr11:58935215-62177656)x3 copy number gain not provided [RCV000683362] Chr11:58935215..62177656 [GRCh37]
Chr11:11q12.1-12.3		 likely pathogenic
GRCh37/hg19 11p15.5-q25(chr11:198510-134934063)x3 copy number gain not provided [RCV000737348] Chr11:198510..134934063 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:70864-134938470)x3 copy number gain not provided [RCV000749874] Chr11:70864..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11q12.2-12.3(chr11:60385382-62456278)x3 copy number gain not provided [RCV001006412] Chr11:60385382..62456278 [GRCh37]
Chr11:11q12.2-12.3		 uncertain significance
GRCh37/hg19 11q12.3(chr11:62010938-62116409)x1 copy number loss not provided [RCV001260129] Chr11:62010938..62116409 [GRCh37]
Chr11:11q12.3		 uncertain significance
GRCh37/hg19 11q12.3(chr11:61874941-62236378)x3 copy number gain not provided [RCV001260130] Chr11:61874941..62236378 [GRCh37]
Chr11:11q12.3		 uncertain significance
NC_000011.9:g.(?_59596957)_(68707199_?)dup duplication Familial temporal lobe epilepsy 8 [RCV001372442] Chr11:59596957..68707199 [GRCh37]
Chr11:11q12.1-13.3		 uncertain significance
Single allele deletion Intellectual disability [RCV001293382] Chr11:118359328..118372573 [GRCh37]
Chr11:11p15.3-q23.3		 pathogenic
NC_000011.9:g.(?_58916346)_(64972349_?)dup duplication Leukocyte adhesion deficiency 3 [RCV003113394]|not provided [RCV003113393] Chr11:58916346..64972349 [GRCh37]
Chr11:11q12.1-13.1		 uncertain significance|no classifications from unflagged records
GRCh37/hg19 11p13-q25(chr11:32799481-134938470)x3 copy number gain MISSED ABORTION [RCV002282973] Chr11:32799481..134938470 [GRCh37]
Chr11:11p13-q25		 pathogenic
NM_206998.2(SCGB1D4):c.47G>A (p.Cys16Tyr) single nucleotide variant not specified [RCV004170233] Chr11:62298964 [GRCh38]
Chr11:62066436 [GRCh37]
Chr11:11q12.3		 uncertain significance
NM_206998.2(SCGB1D4):c.213T>A (p.Phe71Leu) single nucleotide variant not specified [RCV004093976] Chr11:62297501 [GRCh38]
Chr11:62064973 [GRCh37]
Chr11:11q12.3		 likely benign
NM_206998.2(SCGB1D4):c.143A>C (p.Lys48Thr) single nucleotide variant not specified [RCV004163734] Chr11:62297571 [GRCh38]
Chr11:62065043 [GRCh37]
Chr11:11q12.3		 uncertain significance
NM_206998.2(SCGB1D4):c.135A>T (p.Gln45His) single nucleotide variant not specified [RCV004162201] Chr11:62297579 [GRCh38]
Chr11:62065051 [GRCh37]
Chr11:11q12.3		 uncertain significance
GRCh37/hg19 11q12.2-13.5(chr11:59923608-76272324)x3 copy number gain not provided [RCV003484842] Chr11:59923608..76272324 [GRCh37]
Chr11:11q12.2-13.5		 pathogenic
GRCh37/hg19 11q12.1-13.3(chr11:56895955-69295402)x3 copy number gain not specified [RCV003986944] Chr11:56895955..69295402 [GRCh37]
Chr11:11q12.1-13.3		 likely pathogenic
GRCh37/hg19 11p11.12-q13.1(chr11:50398499-63924462)x3 copy number gain not specified [RCV003986918] Chr11:50398499..63924462 [GRCh37]
Chr11:11p11.12-q13.1		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:83
Interacting mature miRNAs:85
Transcripts:ENST00000358585
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.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357380BW64_HBody weight QTL 64 (human)2.2Body weightpercent fat after exercise training116097893786978937Human


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage
High 2
Medium 33
Low 5 1 4 1 9 1 4 5 18 465 3 3
Below cutoff 166 207 148 29 108 18 416 150 831 26 140 142 11 102 289

Sequence


Ensembl Acc Id: ENST00000358585   ⟹   ENSP00000351395
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1162,296,281 - 62,299,075 (-)Ensembl
RefSeq Acc Id: NM_206998   ⟹   NP_996881
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381162,296,281 - 62,299,075 (-)NCBI
GRCh371162,063,754 - 62,066,536 (-)RGD
Build 361161,820,330 - 61,823,112 (-)NCBI Archive
Celera1159,393,130 - 59,395,911 (-)RGD
HuRef1158,392,136 - 58,394,918 (-)RGD
CHM1_11161,946,974 - 61,949,756 (-)NCBI
T2T-CHM13v2.01162,285,567 - 62,288,360 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_996881 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI30640 (Get FASTA)   NCBI Sequence Viewer  
  AAI30646 (Get FASTA)   NCBI Sequence Viewer  
  AAP69948 (Get FASTA)   NCBI Sequence Viewer  
  AAQ89411 (Get FASTA)   NCBI Sequence Viewer  
  EAW74011 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000351395
  ENSP00000351395.1
GenBank Protein Q6XE38 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_996881   ⟸   NM_206998
- Peptide Label: precursor
- UniProtKB: A1L4Q8 (UniProtKB/Swiss-Prot),   Q6XE38 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSP00000351395   ⟸   ENST00000358585

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6XE38-F1-model_v2 AlphaFold Q6XE38 1-83 view protein structure

Promoters
RGD ID:7220635
Promoter ID:EPDNEW_H16062
Type:multiple initiation site
Name:SCGB1D4_1
Description:secretoglobin family 1D member 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381162,299,075 - 62,299,135EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:31748 AgrOrtholog
COSMIC SCGB1D4 COSMIC
Ensembl Genes ENSG00000197745 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000358585 ENTREZGENE
  ENST00000358585.3 UniProtKB/Swiss-Prot
GTEx ENSG00000197745 GTEx
HGNC ID HGNC:31748 ENTREZGENE
Human Proteome Map SCGB1D4 Human Proteome Map
InterPro Secretoglobin UniProtKB/Swiss-Prot
  Secretoglobin_sf UniProtKB/Swiss-Prot
KEGG Report hsa:404552 UniProtKB/Swiss-Prot
NCBI Gene 404552 ENTREZGENE
OMIM 615062 OMIM
PANTHER SECRETOGLOBIN FAMILY 1D UniProtKB/Swiss-Prot
  SECRETOGLOBIN FAMILY 1D MEMBER 4 UniProtKB/Swiss-Prot
Pfam Uteroglobin UniProtKB/Swiss-Prot
PharmGKB PA142670946 PharmGKB
PROSITE SCGB UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48201 UniProtKB/Swiss-Prot
UniProt A1L4Q8 ENTREZGENE
  Q6XE38 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A1L4Q8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-12 SCGB1D4  secretoglobin family 1D member 4    secretoglobin, family 1D, member 4  Symbol and/or name change 5135510 APPROVED