SCGB1D4

secretoglobin family 1D member 4, the group of Secretoglobins

Basic information

Region (hg38): 11:62296281-62299075

Links

ENSG00000197745 ∙ NCBI:404552 ∙ OMIM:615062 ∙ HGNC:31748 ∙ Uniprot:Q6XE38 ∙ 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 SCGB1D4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCGB1D4 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			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	0

Variants in SCGB1D4

This is a list of pathogenic ClinVar variants found in the SCGB1D4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62297501-A-T		not specified	Likely benign (Jun 11, 2021)
11-62297506-A-T		not specified	Uncertain significance (Jan 20, 2025)
11-62297511-T-C		not specified	Uncertain significance (Jul 27, 2024)
11-62297571-T-G		not specified	Uncertain significance (Oct 12, 2022)
11-62297579-T-A		not specified	Uncertain significance (Nov 26, 2024)
11-62297600-A-T		not specified	Uncertain significance (Sep 09, 2024)
11-62297610-A-G		not specified	Uncertain significance (Jan 23, 2025)
11-62298964-C-T		not specified	Uncertain significance (Mar 01, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCGB1D4	protein_coding	protein_coding	ENST00000358585	3	2783

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0575	0.726	125299	0	2	125301	0.00000798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.671	31	43.4	0.714	0.00000220	526
Missense in Polyphen		11	13.781	0.79819		173
Synonymous	-0.0201	19	18.9	1.01	0.00000116	167
Loss of Function	0.777	2	3.59	0.557	1.51e-7	46

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000620	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000332	0.0000329
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to be involved in the regulation of chemotactic cell migration and invasion.

Intolerance Scores

• loftool: 0.727
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.0120
• 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: 0.114

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