SCGB2A1 (secretoglobin family 2A member 1) - Rat Genome Database

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Gene: SCGB2A1 (secretoglobin family 2A member 1) Homo sapiens
Analyze
Symbol: SCGB2A1
Name: secretoglobin family 2A member 1
RGD ID: 1347983
HGNC Page HGNC:7051
Description: Involved in androgen receptor signaling pathway. Located in extracellular space.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: lacryglobin; lipophilin C; lipophilin-C; LPHC; LPNC; mammaglobin 2; mammaglobin B; mammaglobin-2; mammaglobin-B; MGB2; MGC71973; secretoglobin, family 2A, member 1; UGB3
RGD Orthologs
Mouse
Rat
Bonobo
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381162,208,673 - 62,213,943 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1162,208,673 - 62,213,943 (+)EnsemblGRCh38hg38GRCh38
GRCh371161,976,145 - 61,981,415 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361161,732,716 - 61,737,984 (+)NCBINCBI36Build 36hg18NCBI36
Build 341161,732,715 - 61,737,984NCBI
Celera1159,305,589 - 59,310,869 (+)NCBICelera
Cytogenetic Map11q12.3NCBI
HuRef1158,304,514 - 58,309,811 (+)NCBIHuRef
CHM1_11161,859,034 - 61,864,284 (+)NCBICHM1_1
T2T-CHM13v2.01162,197,948 - 62,203,186 (+)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

Biological Process

Cellular Component
extracellular region  (IEA)
extracellular space  (HDA,IBA,IDA,IEA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9504814   PMID:9720917   PMID:9806831   PMID:10066439   PMID:11446459   PMID:12022875   PMID:12477932   PMID:12539042   PMID:12826312   PMID:15151203   PMID:15489334   PMID:16020486  
PMID:16166429   PMID:16395610   PMID:18021217   PMID:18416968   PMID:19635143   PMID:20306663   PMID:21805676   PMID:21873635   PMID:22155607   PMID:22664934   PMID:23332923   PMID:23580065  
PMID:23807163   PMID:24550385   PMID:24585249   PMID:24603286   PMID:24706379   PMID:24823311   PMID:25425335   PMID:25906123   PMID:26186194   PMID:26272612   PMID:27432908   PMID:27705803  
PMID:28514442   PMID:29729704   PMID:31741433   PMID:33961781   PMID:34445801   PMID:34591612   PMID:35833506  


Genomics

Comparative Map Data
SCGB2A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381162,208,673 - 62,213,943 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1162,208,673 - 62,213,943 (+)EnsemblGRCh38hg38GRCh38
GRCh371161,976,145 - 61,981,415 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361161,732,716 - 61,737,984 (+)NCBINCBI36Build 36hg18NCBI36
Build 341161,732,715 - 61,737,984NCBI
Celera1159,305,589 - 59,310,869 (+)NCBICelera
Cytogenetic Map11q12.3NCBI
HuRef1158,304,514 - 58,309,811 (+)NCBIHuRef
CHM1_11161,859,034 - 61,864,284 (+)NCBICHM1_1
T2T-CHM13v2.01162,197,948 - 62,203,186 (+)NCBIT2T-CHM13v2.0
Scgb2a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39199,824,922 - 9,829,564 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl199,824,926 - 9,830,172 (+)EnsemblGRCm39 Ensembl
GRCm38199,847,558 - 9,852,200 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl199,847,562 - 9,852,808 (+)EnsemblGRCm38mm10GRCm38
MGSCv37199,922,106 - 9,926,536 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv37199,922,106 - 9,926,536 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36199,922,106 - 9,926,536 (+)NCBIMGSCv36mm8
Celera1910,544,363 - 10,548,974 (+)NCBICelera
Cytogenetic Map19ANCBI
Scgb2a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81215,922,751 - 215,926,114 (+)NCBIGRCr8
mRatBN7.21206,497,848 - 206,501,211 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1206,369,664 - 206,372,443 (+)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl1206,497,849 - 206,501,211 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1214,879,106 - 214,882,471 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01221,931,385 - 221,934,748 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01214,626,391 - 214,629,754 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01225,899,313 - 225,902,676 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1225,899,313 - 225,902,676 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1225,825,356 - 225,830,355 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01232,850,593 - 232,853,956 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41212,297,718 - 212,301,081 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1203,995,525 - 203,998,888 (+)NCBICelera
Cytogenetic Map1q43NCBI
SCGB2A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2963,439,809 - 63,448,507 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11164,482,829 - 64,491,284 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01157,572,795 - 57,578,901 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11160,930,424 - 60,935,672 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1160,930,424 - 60,935,672 (+)Ensemblpanpan1.1panPan2

Variants

.
Variants in SCGB2A1
6 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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
NM_002407.3(SCGB2A1):c.7C>G (p.Leu3Val) single nucleotide variant Inborn genetic diseases [RCV003278103] Chr11:62208738 [GRCh38]
Chr11:61976210 [GRCh37]
Chr11:11q12.3
uncertain significance
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(chr11:61874941-62236378)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_002407.3(SCGB2A1):c.49T>C (p.Tyr17His) single nucleotide variant Inborn genetic diseases [RCV002906349] Chr11:62208780 [GRCh38]
Chr11:61976252 [GRCh37]
Chr11:11q12.3
uncertain significance
NM_002407.3(SCGB2A1):c.41T>C (p.Leu14Pro) single nucleotide variant Inborn genetic diseases [RCV002845585] Chr11:62208772 [GRCh38]
Chr11:61976244 [GRCh37]
Chr11:11q12.3
uncertain significance
NM_002407.3(SCGB2A1):c.130G>A (p.Glu44Lys) single nucleotide variant Inborn genetic diseases [RCV002738561] Chr11:62210487 [GRCh38]
Chr11:61977959 [GRCh37]
Chr11:11q12.3
uncertain significance
NM_002407.3(SCGB2A1):c.176T>C (p.Met59Thr) single nucleotide variant Inborn genetic diseases [RCV002784985] Chr11:62210533 [GRCh38]
Chr11:61978005 [GRCh37]
Chr11:11q12.3
uncertain significance
NM_002407.3(SCGB2A1):c.143A>T (p.Glu48Val) single nucleotide variant Inborn genetic diseases [RCV003258423] Chr11:62210500 [GRCh38]
Chr11:61977972 [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
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:89
Count of miRNA genes:87
Interacting mature miRNAs:88
Transcripts:ENST00000244930
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-154842  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371161,974,996 - 61,975,274UniSTSGRCh37
Build 361161,731,572 - 61,731,850RGDNCBI36
Celera1159,304,445 - 59,304,723RGD
Cytogenetic Map11q13UniSTS
HuRef1158,303,370 - 58,303,648UniSTS
TNG Radiation Hybrid Map1127338.0UniSTS


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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High 40
Medium 145 2 102 128 1 7 310 3 50 37 207 115 122 6 204
Low 645 13 888 98 106 60 934 11 449 205 325 992 38 1 33 476 1
Below cutoff 402 401 253 166 201 167 555 352 595 75 318 234 5 196 377 1

Sequence


RefSeq Acc Id: ENST00000244930   ⟹   ENSP00000244930
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1162,208,673 - 62,213,943 (+)Ensembl
RefSeq Acc Id: NM_002407   ⟹   NP_002398
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381162,208,673 - 62,213,943 (+)NCBI
GRCh371161,976,140 - 61,981,411 (+)ENTREZGENE
Build 361161,732,716 - 61,737,984 (+)NCBI Archive
HuRef1158,304,514 - 58,309,811 (+)ENTREZGENE
CHM1_11161,859,034 - 61,864,284 (+)NCBI
T2T-CHM13v2.01162,197,948 - 62,203,186 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_002398 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC79996 (Get FASTA)   NCBI Sequence Viewer  
  AAH62218 (Get FASTA)   NCBI Sequence Viewer  
  CAA11865 (Get FASTA)   NCBI Sequence Viewer  
  CAY39335 (Get FASTA)   NCBI Sequence Viewer  
  EAW74008 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000244930
  ENSP00000244930.4
GenBank Protein O75556 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_002398   ⟸   NM_002407
- Peptide Label: precursor
- UniProtKB: O75556 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000244930   ⟸   ENST00000244930

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O75556-F1-model_v2 AlphaFold O75556 1-95 view protein structure

Promoters
RGD ID:7220625
Promoter ID:EPDNEW_H16058
Type:initiation region
Name:SCGB2A1_1
Description:secretoglobin family 2A member 1
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
GRCh381162,208,673 - 62,208,733EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:7051 AgrOrtholog
COSMIC SCGB2A1 COSMIC
Ensembl Genes ENSG00000124939 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000244930 ENTREZGENE
  ENST00000244930.6 UniProtKB/Swiss-Prot
GTEx ENSG00000124939 GTEx
HGNC ID HGNC:7051 ENTREZGENE
Human Proteome Map SCGB2A1 Human Proteome Map
InterPro Secretoglobin UniProtKB/Swiss-Prot
  Secretoglobin_sf UniProtKB/Swiss-Prot
KEGG Report hsa:4246 UniProtKB/Swiss-Prot
NCBI Gene 4246 ENTREZGENE
OMIM 604398 OMIM
PANTHER MAMMAGLOBIN-B UniProtKB/Swiss-Prot
  MAMMAGLOBIN-RELATED UniProtKB/Swiss-Prot
Pfam Uteroglobin UniProtKB/Swiss-Prot
PharmGKB PA34992 PharmGKB
PROSITE SCGB UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48201 UniProtKB/Swiss-Prot
UniProt O75556 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-12 SCGB2A1  secretoglobin family 2A member 1    secretoglobin, family 2A, member 1  Symbol and/or name change 5135510 APPROVED