VPS26C

VPS26 endosomal protein sorting factor C, the group of Retriever complex

Basic information

Region (hg38): 21:37223419-37267919

Previous symbols: [ "DSCR3" ]

Links

ENSG00000157538 ∙ NCBI:10311 ∙ OMIM:605298 ∙ HGNC:3044 ∙ Uniprot:O14972 ∙ 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 VPS26C gene.

• Inborn genetic diseases (4 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS26C 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			5
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	0	0

Variants in VPS26C

This is a list of pathogenic ClinVar variants found in the VPS26C region.

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

Position	Type	Phenotype	Significance	ClinVar
21-37225609-C-T		not specified	Uncertain significance (Dec 27, 2023)
21-37227657-C-T		not specified	Uncertain significance (Nov 20, 2023)
21-37227762-T-C		not specified	Uncertain significance (Jan 16, 2024)
21-37227785-C-T		not specified	Uncertain significance (Aug 10, 2023)
21-37227806-C-T		not specified	Uncertain significance (Nov 17, 2022)
21-37228237-C-T		not specified	Uncertain significance (May 26, 2022)
21-37228256-C-T		not specified	Uncertain significance (Jan 24, 2023)
21-37228312-G-A		not specified	Uncertain significance (Feb 06, 2024)
21-37228345-C-T		not specified	Uncertain significance (Aug 08, 2022)
21-37232411-G-A		not specified	Uncertain significance (Nov 07, 2022)
21-37232424-G-C		not specified	Uncertain significance (Dec 20, 2023)
21-37233418-G-A		not specified	Uncertain significance (Nov 07, 2022)
21-37238597-T-C		not specified	Uncertain significance (Jan 26, 2022)
21-37238599-A-G		not specified	Uncertain significance (Sep 27, 2022)
21-37238601-C-A		not specified	Uncertain significance (Mar 08, 2024)
21-37238604-G-C		not specified	Uncertain significance (Feb 16, 2023)
21-37240519-C-A			Uncertain significance (Aug 13, 2020)
21-37240611-G-A		not specified	Uncertain significance (Jun 27, 2022)
21-37240615-T-C		VPS26C-related disorder	Likely benign (Apr 24, 2023)
21-37240623-A-G		not specified	Uncertain significance (Dec 14, 2022)
21-37267284-G-T		not specified	Uncertain significance (Nov 07, 2022)
21-37267290-C-T		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPS26C	protein_coding	protein_coding	ENST00000309117	8	44542

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000149	0.878	125726	0	21	125747	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	143	186	0.770	0.0000112	1942
Missense in Polyphen		53	71.944	0.73668		743
Synonymous	0.439	74	79.0	0.937	0.00000554	586
Loss of Function	1.41	8	13.6	0.588	6.39e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.120

Intolerance Scores

• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.143
• hipred: Y
• hipred_score: 0.717
• ghis: 0.626

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Vps26c