WASHC3

WASH complex subunit 3, the group of WASH complex

Basic information

Region (hg38): 12:102012840-102062149

Previous symbols: [ "CCDC53" ]

Links

ENSG00000120860 ∙ NCBI:51019 ∙ OMIM:619925 ∙ HGNC:24256 ∙ Uniprot:Q9Y3C0 ∙ 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 WASHC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WASHC3 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			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	0

Variants in WASHC3

This is a list of pathogenic ClinVar variants found in the WASHC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-102013127-T-G		not specified	Uncertain significance (Dec 20, 2023)
12-102039933-C-T		not specified	Uncertain significance (Jan 23, 2024)
12-102039968-G-A		not specified	Uncertain significance (Jul 26, 2023)
12-102044181-G-T		not specified	Uncertain significance (Nov 21, 2022)
12-102044185-C-G		not specified	Uncertain significance (Feb 11, 2022)
12-102046095-T-C		not specified	Uncertain significance (May 31, 2023)
12-102046104-A-C		not specified	Uncertain significance (Oct 05, 2023)
12-102061262-T-C		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WASHC3	protein_coding	protein_coding	ENST00000240079	7	49223

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00457	0.885	124610	0	26	124636	0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.433	80	91.7	0.873	0.00000431	1245
Missense in Polyphen		24	30.502	0.78683		430
Synonymous	-1.53	41	30.3	1.35	0.00000142	371
Loss of Function	1.36	5	9.52	0.525	4.03e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000301	0.000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000605	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000150
Middle Eastern	0.0000605	0.0000556
South Asian	0.0000334	0.0000327
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts at least in part as component of the WASH core complex whose assembly at the surface of endosomes seems to inhibit WASH nucleation-promoting factor (NPF) activity in recruiting and activating the Arp2/3 complex to induce actin polymerization, and which is involved in regulation of the fission of tubules that serve as transport intermediates during endosome sorting (PubMed:19922875, PubMed:20498093). {ECO:0000269|PubMed:19922875, ECO:0000269|PubMed:20498093}.
• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.221
• hipred: N
• hipred_score: 0.292
• ghis: 0.509

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Washc3

Gene ontology

• Biological process: exocytosis;biological_process;protein transport;actin filament polymerization
• Cellular component: early endosome;WASH complex
• Molecular function: protein binding