WRAP73

WD repeat containing, antisense to TP73, the group of WD repeat domain containing

Basic information

Region (hg38): 1:3630767-3652761

Previous symbols: [ "WDR8" ]

Links

ENSG00000116213 ∙ NCBI:49856 ∙ OMIM:606040 ∙ HGNC:12759 ∙ Uniprot:Q9P2S5 ∙ 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 WRAP73 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WRAP73 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
missense			34	1		35
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	2	0

Variants in WRAP73

This is a list of pathogenic ClinVar variants found in the WRAP73 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-3630979-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-3630994-T-A		not specified	Uncertain significance (Aug 13, 2021)
1-3631010-C-T		not specified	Likely benign (Mar 06, 2023)
1-3631069-A-G		not specified	Uncertain significance (Sep 13, 2023)
1-3631522-C-T		not specified	Uncertain significance (Apr 05, 2023)
1-3631547-G-A		not specified	Uncertain significance (Apr 20, 2024)
1-3631549-G-A		not specified	Uncertain significance (May 26, 2023)
1-3631576-C-G		not specified	Uncertain significance (May 21, 2024)
1-3631601-C-T		not specified	Uncertain significance (Apr 04, 2023)
1-3631642-G-A		not specified	Uncertain significance (Aug 22, 2023)
1-3631643-C-T		not specified	Uncertain significance (Apr 20, 2024)
1-3631651-A-G		not specified	Uncertain significance (Dec 08, 2023)
1-3632243-G-A		not specified	Uncertain significance (Apr 04, 2024)
1-3632275-G-A		not specified	Uncertain significance (May 17, 2023)
1-3632288-C-G		not specified	Uncertain significance (Dec 15, 2023)
1-3632290-G-A		not specified	Uncertain significance (Nov 28, 2023)
1-3632329-G-A		not specified	Uncertain significance (Feb 10, 2022)
1-3633431-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-3633442-G-A		not specified	Uncertain significance (Feb 10, 2023)
1-3633478-C-A		not specified	Uncertain significance (May 04, 2023)
1-3633493-T-C		not specified	Uncertain significance (Sep 06, 2022)
1-3635017-C-A		not specified	Uncertain significance (Sep 12, 2023)
1-3635031-A-C		not specified	Uncertain significance (Jun 17, 2024)
1-3635173-C-T		not specified	Uncertain significance (Oct 18, 2021)
1-3635288-T-A		not specified	Uncertain significance (Nov 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WRAP73	protein_coding	protein_coding	ENST00000270708	12	21995

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000150	0.992	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00715	291	291	0.999	0.0000190	2970
Missense in Polyphen		49	57.525	0.8518		561
Synonymous	-0.754	145	134	1.08	0.0000102	896
Loss of Function	2.38	14	27.4	0.510	0.00000125	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000182
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000215	0.000211
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The SSX2IP:WRAP73 complex is proposed to act as regulator of spindle anchoring at the mitotic centrosome. Required for the centrosomal localization of SSX2IP and normal mitotic bipolar spindle morphology (PubMed:26545777). Required for the targeting of centriole satellite proteins to centrosomes such as of PCM1, SSX2IP, CEP290 and PIBF1/CEP90. Required for ciliogenesis and involved in the removal of the CEP97:CCP110 complex from the mother centriole. Involved in ciliary vesicle formation at the mother centriole and required for the docking of vesicles to the basal body during ciliogenesis; may promote docking of RAB8A- and ARL13B-containing vesicles (PubMed:26675238). {ECO:0000269|PubMed:26545777, ECO:0000269|PubMed:26675238}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.68

Haploinsufficiency Scores

• pHI: 0.263
• hipred: Y
• hipred_score: 0.535
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wrap73

Gene ontology

• Biological process: cell projection organization;mitotic spindle assembly;positive regulation of non-motile cilium assembly
• Cellular component: centrosome;centriole;ciliary basal body
• Molecular function: protein binding