SCGB1D2

secretoglobin family 1D member 2, the group of Secretoglobins

Basic information

Region (hg38): 11:62242239-62244812

Links

ENSG00000124935 ∙ NCBI:10647 ∙ OMIM:615061 ∙ HGNC:18396 ∙ Uniprot:O95969 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCGB1D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCGB1D2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	1

Variants in SCGB1D2

This is a list of pathogenic ClinVar variants found in the SCGB1D2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-62242318-C-T		not specified	Uncertain significance (Feb 28, 2025)
11-62243303-T-C		not specified	Uncertain significance (Mar 06, 2023)
11-62243327-T-G		not specified	Uncertain significance (Aug 26, 2022)
11-62243335-C-A		not specified	Uncertain significance (Nov 25, 2024)
11-62243355-T-A		not specified	Uncertain significance (Apr 12, 2023)
11-62243370-T-C		not specified	Uncertain significance (Jun 06, 2023)
11-62243385-C-T		not specified	Uncertain significance (Feb 22, 2023)
11-62243402-G-A		not specified	Uncertain significance (Oct 01, 2024)
11-62243467-G-A			Benign (Mar 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCGB1D2	protein_coding	protein_coding	ENST00000244926	3	2599

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.270	0.643	125727	0	4	125731	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.380	55	47.6	1.16	0.00000244	574
Missense in Polyphen		23	17.28	1.331		211
Synonymous	-0.672	25	21.1	1.19	0.00000123	174
Loss of Function	1.28	1	3.64	0.275	1.52e-7	49

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000331	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May bind androgens and other steroids, may also bind estramustine, a chemotherapeutic agent used for prostate cancer. May be under transcriptional regulation of steroid hormones.

Intolerance Scores

• loftool: 0.687
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.00801
• hipred: N
• hipred_score: 0.112
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0135

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Cellular component: extracellular space