SCGB1D1

secretoglobin family 1D member 1, the group of Secretoglobins

Basic information

Region (hg38): 11:62190216-62193539

Links

ENSG00000168515

∙ NCBI:10648 ∙ OMIM:615060 ∙ HGNC:18395 ∙ Uniprot:O95968 ∙ 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 SCGB1D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCGB1D1 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						0
missense			9 clinvar			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in SCGB1D1

This is a list of pathogenic ClinVar variants found in the SCGB1D1 region.

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

Position	Phenotype	Significance	ClinVar
11-62190297-G-A	not specified	Uncertain significance (Nov 14, 2024)	3438007
11-62190321-G-A	not specified	Uncertain significance (Feb 17, 2022)	2277484
11-62190328-G-T	not specified	Uncertain significance (Oct 25, 2024)	3438006
11-62190333-T-C	not specified	Uncertain significance (May 01, 2024)	2385763
11-62192082-G-T	not specified	Uncertain significance (Jul 09, 2021)	2392811
11-62192131-T-C	not specified	Uncertain significance (Dec 20, 2023)	3158403
11-62192145-T-A	not specified	Uncertain significance (Jul 19, 2022)	2388451
11-62193423-C-T	not specified	Uncertain significance (Dec 05, 2024)	3438008
11-62193424-G-A	not specified	Uncertain significance (Jan 16, 2024)	3158404

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCGB1D1	protein_coding	protein_coding	ENST00000306238	3	3324

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.29e-7	0.0322	125672	1	63	125736	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.139	51	48.3	1.06	0.00000254	566
Missense in Polyphen		7	10.813	0.64737		135
Synonymous	0.0609	20	20.3	0.983	0.00000119	181
Loss of Function	-2.15	8	3.60	2.22	1.52e-7	48

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000876	0.0000876
Ashkenazi Jewish	0.000695	0.000695
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000335	0.000334
Middle Eastern	0.00	0.00
South Asian	0.000428	0.000392
Other	0.000652	0.000652

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.;

Recessive Scores

pRec: 0.0241

Intolerance Scores

loftool: 0.743
rvis_EVS: 0.53
rvis_percentile_EVS: 80.58

Haploinsufficiency Scores

pHI: 0.00165
hipred: N
hipred_score: 0.112
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Lipa
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
Cellular component: extracellular space
Molecular function: protein heterodimerization activity