WSCD2

WSC domain containing 2

Basic information

Region (hg38): 12:108129287-108250537

Links

ENSG00000075035 ∙ NCBI:9671 ∙ OMIM:619253 ∙ HGNC:29117 ∙ Uniprot:Q2TBF2 ∙ 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 WSCD2 gene.

• Inborn genetic diseases (25 variants)
• not provided (4 variants)
• Marfanoid habitus and intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WSCD2 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			26		1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	2

Variants in WSCD2

This is a list of pathogenic ClinVar variants found in the WSCD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-108195885-G-A		not specified	Uncertain significance (Aug 13, 2021)
12-108195925-C-A		not specified	Uncertain significance (Dec 14, 2023)
12-108195962-G-A		not specified	Uncertain significance (Feb 26, 2024)
12-108196007-G-A		not specified	Uncertain significance (Jan 29, 2024)
12-108196038-A-T		not specified	Uncertain significance (Feb 03, 2022)
12-108196070-G-A		not specified	Uncertain significance (Jun 16, 2023)
12-108196079-T-C		not specified	Uncertain significance (Dec 16, 2023)
12-108196091-C-T		not specified	Uncertain significance (Dec 16, 2022)
12-108196170-G-C		not specified	Uncertain significance (Aug 08, 2022)
12-108196194-G-A		not specified	Uncertain significance (Aug 09, 2021)
12-108206337-G-A		not specified	Uncertain significance (Jul 09, 2021)
12-108206364-A-G		not specified	Uncertain significance (Nov 03, 2023)
12-108206364-A-T		not specified	Uncertain significance (Apr 22, 2022)
12-108206378-C-T		not specified	Uncertain significance (Mar 24, 2023)
12-108210251-G-A		Marfanoid habitus and intellectual disability	Uncertain significance (-)
12-108210257-C-T		not specified	Uncertain significance (Jul 06, 2022)
12-108210300-G-T		not specified	Uncertain significance (Mar 23, 2023)
12-108224776-C-G			Likely benign (Mar 01, 2023)
12-108224777-G-A		not specified	Uncertain significance (Nov 03, 2023)
12-108224790-T-A		not specified	Uncertain significance (Oct 03, 2022)
12-108224853-C-T			Benign (Jul 13, 2018)
12-108226993-T-C		not specified	Uncertain significance (Sep 17, 2021)
12-108226997-C-T		not specified	Uncertain significance (Jun 02, 2023)
12-108227018-C-A		not specified	Uncertain significance (May 25, 2022)
12-108227054-C-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WSCD2	protein_coding	protein_coding	ENST00000332082	8	121067

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.783	0.217	124966	0	24	124990	0.0000960

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	293	368	0.796	0.0000248	3695
Missense in Polyphen		88	121.6	0.72366		1203
Synonymous	0.190	148	151	0.980	0.0000106	1112
Loss of Function	3.93	5	27.0	0.185	0.00000148	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000111	0.000111
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.0000840	0.0000794
Middle Eastern	0.000111	0.000111
South Asian	0.000198	0.000196
Other	0.000340	0.000329

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.494
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.78

Haploinsufficiency Scores

• pHI: 0.224
• hipred: Y
• hipred_score: 0.714
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wscd2

Gene ontology

• Cellular component: integral component of membrane