WASHC2A

WASH complex subunit 2A, the group of WASH complex

Basic information

Region (hg38): 10:50067888-50133509

Previous symbols: [ "FAM21B", "FAM21A" ]

Links

ENSG00000099290 ∙ NCBI:387680 ∙ ∙ HGNC:23416 ∙ Uniprot:Q641Q2 ∙ 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 WASHC2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WASHC2A 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			39	6		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	7	0

Variants in WASHC2A

This is a list of pathogenic ClinVar variants found in the WASHC2A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-50068106-T-C		not specified	Uncertain significance (Nov 15, 2024)
10-50068144-T-G		not specified	Uncertain significance (May 14, 2024)
10-50068150-C-T		not specified	Uncertain significance (May 10, 2022)
10-50068169-G-T		not specified	Uncertain significance (Jun 26, 2024)
10-50068197-C-A		not specified	Uncertain significance (Dec 02, 2022)
10-50069553-C-G		not specified	Uncertain significance (Dec 06, 2024)
10-50069652-C-T		not specified	Uncertain significance (Sep 17, 2021)
10-50092188-C-T		not specified	Uncertain significance (Sep 27, 2024)
10-50092198-T-C		not specified	Uncertain significance (May 01, 2024)
10-50092216-G-A		not specified	Uncertain significance (Feb 15, 2023)
10-50093276-G-C		not specified	Uncertain significance (Aug 17, 2022)
10-50093279-A-G		not specified	Uncertain significance (Nov 11, 2024)
10-50093295-C-G		not specified	Uncertain significance (Apr 30, 2024)
10-50093306-G-A		not specified	Uncertain significance (Jun 30, 2023)
10-50093351-G-T		not specified	Uncertain significance (Dec 16, 2023)
10-50093355-G-T		not specified	Uncertain significance (Mar 07, 2023)
10-50093372-G-A		not specified	Uncertain significance (Mar 07, 2024)
10-50093372-G-C		not specified	Uncertain significance (Jul 02, 2024)
10-50093881-C-T		not specified	Uncertain significance (Jan 02, 2024)
10-50093890-C-T		not specified	Uncertain significance (Jul 12, 2022)
10-50093911-A-C		not specified	Uncertain significance (Sep 27, 2022)
10-50095201-T-G		not specified	Uncertain significance (Oct 26, 2021)
10-50095637-A-C		not specified	Likely benign (Jul 09, 2021)
10-50095689-G-A		not specified	Uncertain significance (Apr 01, 2022)
10-50095760-A-T		not specified	Uncertain significance (Jun 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WASHC2A	protein_coding	protein_coding	ENST00000282633	31	65622

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000463	0.993	124119	58	617	124794	0.00271

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.659	210	239	0.880	0.0000125	8756
Missense in Polyphen		73	90.048	0.81068		3416
Synonymous	0.707	84	92.7	0.907	0.00000509	2495
Loss of Function	2.39	9	20.7	0.434	8.91e-7	841

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00254	0.00222
Ashkenazi Jewish	0.00412	0.00338
East Asian	0.00	0.00
Finnish	0.00189	0.00153
European (Non-Finnish)	0.00552	0.00438
Middle Eastern	0.00	0.00
South Asian	0.00186	0.00154
Other	0.00239	0.00215

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts at least in part as component of the WASH core complex whose assembly at the surface of endosomes inhibits WASH nucleation-promoting factor (NPF) activity in recruiting and activating the Arp2/3 complex to induce actin polymerization and is involved in the fission of tubules that serve as transport intermediates during endosome sorting. Mediates the recruitment of the WASH core complex to endosome membranes via binding to phospholipids and VPS35 of the retromer CSC. Mediates the recruitment of the F-actin-capping protein dimer to the WASH core complex probably promoting localized F-actin polymerization needed for vesicle scission. Via its C-terminus binds various phospholipids, most strongly phosphatidylinositol 4-phosphate (PtdIns-(4)P), phosphatidylinositol 5-phosphate (PtdIns-(5)P) and phosphatidylinositol 3,5-bisphosphate (PtdIns-(3,5)P2). Involved in the endosome-to-plasma membrane trafficking and recycling of SNX27-retromer-dependent cargo proteins, such as GLUT1. Required for the association of DNAJC13, ENTR1, ANKRD50 with retromer CSC subunit VPS35. Required for the endosomal recruitment of CCC complex subunits COMMD1, CCDC93 and C16orf62. Plays a role in fluid-phase endocytosis, a process exploited by vaccinia intracellular mature virus (IMV) to enter cells. As a result, may facilitate the penetration of IMV into cells (By similarity). {ECO:0000250|UniProtKB:Q9Y4E1}.
• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.431
• ghis: 0.516

Essentials

• essential_gene_gene_trap: N

Gene ontology

• Biological process: protein transport;retrograde transport, endosome to Golgi
• Cellular component: nucleolus;early endosome;cytosol;plasma membrane;early endosome membrane;intracellular membrane-bounded organelle;WASH complex
• Molecular function: protein binding;lipid binding