WASH4P

WASP family homolog 4, pseudogene, the group of Wiskott-Aldrich Syndrome protein family

Basic information

Region (hg38): 16:14381-18068

Previous symbols: [ "FAM39CP" ]

Links

ENSG00000234769 ∙ NCBI:374677 ∙ ∙ HGNC:14126 ∙ Uniprot:A8MWX3 ∙ 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 WASH4P gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WASH4P 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	0	1	0

Variants in WASH4P

This is a list of pathogenic ClinVar variants found in the WASH4P region.

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

Position	Type	Phenotype	Significance	ClinVar
16-14494-G-A			Likely benign (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WASH4P	protein_coding	protein_coding	ENST00000326592	10	5410

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00234	0.784	105753	0	5	105758	0.0000236

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.342	132	121	1.09	0.00000705	2924
Missense in Polyphen		48	38.803	1.237		857
Synonymous	-1.05	58	48.7	1.19	0.00000292	905
Loss of Function	0.997	5	8.05	0.621	3.41e-7	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000233	0.000229
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000233	0.000229
South Asian	0.00	0.00
Other	0.000190	0.000189

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a nucleation-promoting factor at the surface of endosomes, where it recruits and activates the Arp2/3 complex to induce actin polymerization, playing a key role in the fission of tubules that serve as transport intermediates during endosome sorting. {ECO:0000250|UniProtKB:A8K0Z3, ECO:0000250|UniProtKB:C4AMC7}.

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.209
• ghis: 0.501

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.0443

Gene Damage Prediction

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

Gene ontology

• Biological process: endosomal transport;Arp2/3 complex-mediated actin nucleation;retrograde transport, endosome to Golgi
• Cellular component: early endosome;cytosol;early endosome membrane;recycling endosome;recycling endosome membrane;WASH complex
• Molecular function: actin binding;alpha-tubulin binding