WDCP

WD repeat and coiled coil containing, the group of MRN complex

Basic information

Region (hg38): 2:24029346-24049575

Previous symbols: [ "C2orf44" ]

Links

ENSG00000163026 ∙ NCBI:80304 ∙ OMIM:616234 ∙ HGNC:26157 ∙ Uniprot:Q9H6R7 ∙ 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 WDCP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDCP 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in WDCP

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

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

Position	Type	Phenotype	Significance	ClinVar
2-24037829-G-C		not specified	Uncertain significance (Aug 09, 2021)
2-24037858-T-C		not specified	Uncertain significance (Nov 27, 2023)
2-24037940-T-C		not specified	Uncertain significance (Aug 02, 2021)
2-24038675-A-G		not specified	Uncertain significance (Oct 06, 2021)
2-24038895-A-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDCP	protein_coding	protein_coding	ENST00000295148	3	20236

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00102	0.989	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.479	354	380	0.931	0.0000186	4710
Missense in Polyphen		75	104.08	0.7206		1404
Synonymous	0.709	137	148	0.926	0.00000766	1505
Loss of Function	2.25	8	18.4	0.434	8.42e-7	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00254	0.00254
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.000328	0.000327
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=A chromosomal aberration involving WDCP is found in one subject with colorectal cancer. Translocation t(2;2)(p23.3;p23.1). A 5 million base pair tandem duplication generates an in-frame WDCP-ALK gene fusion. {ECO:0000269|PubMed:22327622}.
• Pathway: Mesodermal Commitment Pathway (Consensus)

Recessive Scores

• pRec: 0.0841

Intolerance Scores

• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.13

Haploinsufficiency Scores

• pHI: 0.243
• hipred: N
• hipred_score: 0.456
• ghis: 0.518

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Wdcp

Gene ontology

• Biological process: protein complex oligomerization
• Molecular function: kinase binding