WTAP

WT1 associated protein, the group of WTAP complex|m6A methyltransferase complex

Basic information

Region (hg38): 6:159725584-159756319

Links

ENSG00000146457 ∙ NCBI:9589 ∙ OMIM:605442 ∙ HGNC:16846 ∙ Uniprot:Q15007 ∙ 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 WTAP gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

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

Variants in WTAP

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

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

Position	Type	Phenotype	Significance	ClinVar
6-159748228-G-C		not specified	Uncertain significance (May 27, 2022)
6-159748286-A-T		not specified	Uncertain significance (Apr 22, 2022)
6-159755210-G-A		not specified	Uncertain significance (Dec 27, 2022)
6-159755211-A-G		not specified	Uncertain significance (Dec 27, 2022)
6-159755213-G-A		not specified	Uncertain significance (May 06, 2022)
6-159755270-C-T		not specified	Uncertain significance (Apr 08, 2022)
6-159755280-C-T		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WTAP	protein_coding	protein_coding	ENST00000358372	7	30735

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000335	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	121	215	0.564	0.0000114	2612
Missense in Polyphen		24	49.169	0.48811		681
Synonymous	-0.581	88	81.3	1.08	0.00000462	733
Loss of Function	4.44	0	22.9	0.00	0.00000126	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000664	0.0000664
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000534	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing (PubMed:29507755). Required for accumulation of METTL3 and METTL14 to nuclear speckle (PubMed:24316715, PubMed:24407421, PubMed:24981863). Acts as a mRNA splicing regulator (PubMed:12444081). Regulates G2/M cell-cycle transition by binding to the 3' UTR of CCNA2, which enhances its stability (PubMed:17088532). Impairs WT1 DNA-binding ability and inhibits expression of WT1 target genes (PubMed:17095724). {ECO:0000269|PubMed:12444081, ECO:0000269|PubMed:17088532, ECO:0000269|PubMed:17095724, ECO:0000269|PubMed:24316715, ECO:0000269|PubMed:24407421, ECO:0000269|PubMed:24981863, ECO:0000269|PubMed:29507755}.
• Pathway: Metabolism of RNA;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.345
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.233
• hipred: Y
• hipred_score: 0.794
• ghis: 0.555

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wtap
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: wtap
• Affected structure: ventricular system
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA processing;cell cycle;multicellular organism development;RNA splicing;mRNA methylation
• Cellular component: nucleus;nucleoplasm;cytoplasm;nuclear speck;nuclear membrane;RNA N6-methyladenosine methyltransferase complex
• Molecular function: protein binding