WWC3

WWC family member 3, the group of WWC family

Basic information

Region (hg38): X:10015253-10144474

Links

ENSG00000047644 ∙ NCBI:55841 ∙ OMIM:301089 ∙ HGNC:29237 ∙ Uniprot:Q9ULE0 ∙ 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 WWC3 gene.

• Inborn genetic diseases (35 variants)
• not provided (24 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WWC3 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				10	4	14
missense			34	5	4	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	15	8

Variants in WWC3

This is a list of pathogenic ClinVar variants found in the WWC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-10067337-C-T		not specified	Uncertain significance (Nov 30, 2021)
X-10067359-T-C		not specified	Uncertain significance (Feb 10, 2022)
X-10067380-A-G		not specified	Uncertain significance (Jul 14, 2022)
X-10067421-G-A			Benign (May 07, 2018)
X-10067474-C-A		not specified	Uncertain significance (Feb 10, 2022)
X-10067476-G-A		not specified	Uncertain significance (Jan 24, 2024)
X-10067484-G-A		not specified	Uncertain significance (May 01, 2022)
X-10094215-G-C			Likely benign (Jul 01, 2022)
X-10094249-G-A		not specified	Uncertain significance (Dec 06, 2022)
X-10094276-G-A		not specified	Uncertain significance (Feb 06, 2024)
X-10109838-C-T			Likely benign (Oct 01, 2022)
X-10109842-G-A		not specified	Uncertain significance (Aug 10, 2021)
X-10109855-G-A		not specified	Uncertain significance (Feb 13, 2024)
X-10109855-G-T		not specified	Uncertain significance (Sep 20, 2023)
X-10109895-G-C		not specified	Uncertain significance (Oct 05, 2023)
X-10109915-A-G		not specified	Uncertain significance (Feb 28, 2023)
X-10109916-G-A			Benign (Apr 10, 2018)
X-10109962-C-T		not specified	Uncertain significance (Apr 18, 2023)
X-10109984-G-A		not specified	Uncertain significance (Jul 25, 2023)
X-10110000-C-T			Likely benign (Aug 01, 2022)
X-10110010-G-A		not specified	Uncertain significance (Dec 14, 2023)
X-10110014-C-T		not specified	Uncertain significance (Apr 08, 2022)
X-10117144-C-T		not specified	Uncertain significance (Jan 09, 2024)
X-10117165-G-A		not specified	Uncertain significance (Sep 07, 2022)
X-10117206-C-T		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WWC3	protein_coding	protein_coding	ENST00000380861	22	128917

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000377	125742	3	3	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	424	521	0.813	0.0000496	7024
Missense in Polyphen		113	181.09	0.62398		2470
Synonymous	-0.385	241	234	1.03	0.0000231	2259
Loss of Function	5.58	3	42.0	0.0714	0.00000336	642

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000625	0.0000462
European (Non-Finnish)	0.0000747	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0826

Intolerance Scores

• loftool: 0.165
• rvis_EVS: 0.72
• rvis_percentile_EVS: 85.85

Haploinsufficiency Scores

• pHI: 0.134
• hipred: Y
• hipred_score: 0.626
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.186

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;negative regulation of hippo signaling;negative regulation of organ growth
• Cellular component: cytosol
• Molecular function: kinase binding;protein-containing complex scaffold activity