WSCD1

WSC domain containing 1

Basic information

Region (hg38): 17:6057806-6124427

Links

ENSG00000179314 ∙ NCBI:23302 ∙ OMIM:619584 ∙ HGNC:29060 ∙ Uniprot:Q658N2 ∙ 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 WSCD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WSCD1 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				3		3
missense			56	3		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	6	0

Variants in WSCD1

This is a list of pathogenic ClinVar variants found in the WSCD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-6069271-G-A			Likely benign (Sep 01, 2022)
17-6080662-G-A		not specified	Uncertain significance (Jan 26, 2022)
17-6080663-C-A		not specified	Uncertain significance (Jan 26, 2022)
17-6080699-G-A		not specified	Uncertain significance (Nov 22, 2023)
17-6080746-G-A		not specified	Uncertain significance (Aug 23, 2021)
17-6080774-G-A		not specified	Uncertain significance (May 13, 2022)
17-6080798-G-C		not specified	Uncertain significance (Jun 07, 2023)
17-6080815-C-A		not specified	Uncertain significance (Mar 28, 2024)
17-6080827-G-A		not specified	Uncertain significance (Dec 16, 2023)
17-6080840-C-T		not specified	Uncertain significance (Nov 22, 2022)
17-6080848-G-A		not specified	Uncertain significance (Dec 17, 2021)
17-6080917-A-G		not specified	Likely benign (Oct 16, 2023)
17-6080944-C-T		not specified	Uncertain significance (Jun 23, 2023)
17-6080956-C-T		not specified	Uncertain significance (Mar 06, 2023)
17-6080965-C-T		not specified	Uncertain significance (Aug 10, 2021)
17-6080966-G-A		not specified	Uncertain significance (Sep 20, 2023)
17-6080970-C-A		not specified	Uncertain significance (May 05, 2023)
17-6080987-G-A		not specified	Uncertain significance (Sep 21, 2021)
17-6080989-C-A		not specified	Uncertain significance (Mar 14, 2023)
17-6081014-A-G		not specified	Uncertain significance (Sep 16, 2021)
17-6081055-G-A		not specified	Uncertain significance (Dec 08, 2023)
17-6081083-G-A		not specified	Uncertain significance (Oct 12, 2021)
17-6088025-G-A		not specified	Uncertain significance (Jun 07, 2024)
17-6088064-A-G		not specified	Uncertain significance (Jun 21, 2021)
17-6090336-C-T			Likely benign (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WSCD1	protein_coding	protein_coding	ENST00000574946	8	352194

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000636	0.999	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.543	359	389	0.922	0.0000283	3670
Missense in Polyphen		117	139.47	0.83887		1443
Synonymous	-1.28	186	165	1.13	0.0000118	1206
Loss of Function	2.88	12	28.6	0.419	0.00000180	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000511	0.000510
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.000167	0.000163
South Asian	0.000501	0.000490
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.334
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.98

Haploinsufficiency Scores

• pHI: 0.573
• hipred: Y
• hipred_score: 0.507
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wscd1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: sulfotransferase activity