WHAMM

WASP homolog associated with actin, golgi membranes and microtubules, the group of Wiskott-Aldrich Syndrome protein family

Basic information

Region (hg38): 15:82809628-82836108

Previous symbols: [ "WHDC1" ]

Links

ENSG00000156232 ∙ NCBI:123720 ∙ OMIM:612393 ∙ HGNC:30493 ∙ Uniprot:Q8TF30 ∙ 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 WHAMM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WHAMM 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	2
missense			63	3	1	67
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	63	4	2

Variants in WHAMM

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

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

Position	Type	Phenotype	Significance	ClinVar
15-82809864-C-G		not specified	Uncertain significance (Jul 14, 2024)
15-82809913-C-T		not specified	Uncertain significance (Oct 12, 2024)
15-82809932-C-T		not specified	Uncertain significance (Feb 06, 2024)
15-82809974-C-T		not specified	Uncertain significance (Aug 14, 2023)
15-82809983-G-A		not specified	Uncertain significance (Nov 06, 2023)
15-82809985-C-G		not specified	Uncertain significance (Nov 11, 2024)
15-82810057-G-C		not specified	Uncertain significance (Jul 07, 2023)
15-82810061-T-G		not specified	Uncertain significance (Sep 25, 2023)
15-82810066-G-A		not specified	Uncertain significance (Jul 25, 2023)
15-82810076-G-A		not specified	Uncertain significance (Sep 14, 2022)
15-82810099-G-T		not specified	Uncertain significance (Mar 17, 2023)
15-82810119-G-C		not specified	Uncertain significance (Mar 17, 2023)
15-82810135-C-T		not specified	Uncertain significance (Jul 12, 2022)
15-82810151-T-G		not specified	Uncertain significance (May 25, 2022)
15-82810181-A-C		not specified	Uncertain significance (Apr 17, 2023)
15-82810195-G-A		not specified	Uncertain significance (Jun 21, 2022)
15-82810198-G-A		not specified	Uncertain significance (Mar 25, 2024)
15-82810237-C-T		not specified	Uncertain significance (Oct 20, 2023)
15-82810238-C-T		not specified	Uncertain significance (Dec 19, 2022)
15-82810249-G-T		not specified	Uncertain significance (May 06, 2024)
15-82810292-C-A		not specified	Uncertain significance (Nov 27, 2024)
15-82810292-C-T		not specified	Uncertain significance (May 25, 2022)
15-82813133-A-G		not specified	Uncertain significance (May 03, 2023)
15-82813226-C-A		not specified	Uncertain significance (Nov 09, 2024)
15-82813227-C-T		Premature ovarian failure	Uncertain significance (Mar 02, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WHAMM	protein_coding	protein_coding	ENST00000286760	10	25232

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.81e-13	0.184	124588	0	65	124653	0.000261

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.180	367	357	1.03	0.0000197	5142
Missense in Polyphen		120	115.82	1.0361		1700
Synonymous	-1.40	161	140	1.15	0.00000793	1624
Loss of Function	0.931	22	27.2	0.808	0.00000147	404

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000421	0.000419
Ashkenazi Jewish	0.000103	0.0000994
East Asian	0.000461	0.000389
Finnish	0.000280	0.000278
European (Non-Finnish)	0.000195	0.000186
Middle Eastern	0.000461	0.000389
South Asian	0.000691	0.000621
Other	0.000345	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a nucleation-promoting factor (NPF) that stimulates Arp2/3-mediated actin polymerization both at the Golgi apparatus and along tubular membranes. Its activity in membrane tubulation requires F-actin and interaction with microtubules. Proposed to use coordinated actin-nucleating and microtubule- binding activities of distinct WHAMM molecules to drive membrane tubule elongation; when MT-bound can recruit and remodel membrane vesicles but is prevented to activate the Arp2/3 complex. Involved as a regulator of Golgi positioning and morphology. Participates in vesicle transport between the reticulum endoplasmic and the Golgi complex. Required for RhoD-dependent actin reorganization such as in cell adhesion and cell migration. {ECO:0000269|PubMed:18614018, ECO:0000269|PubMed:23027905, ECO:0000269|PubMed:23087206}.
• Pathway: Tight junction - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0950

Intolerance Scores

• loftool: 0.899
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.65

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.162
• ghis: 0.491

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.382

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Whamm

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;actin filament organization;cell cycle arrest;lamellipodium assembly;Arp2/3 complex-mediated actin nucleation;focal adhesion assembly;positive regulation of actin nucleation;actin filament reorganization;plasma membrane tubulation
• Cellular component: Golgi membrane;cytoplasm;cytosol;microtubule;cytoplasmic vesicle membrane;endoplasmic reticulum-Golgi intermediate compartment membrane
• Molecular function: actin binding;microtubule binding;GTP-Rho binding;Arp2/3 complex binding