Is WDR62 p.Trp186Ter (c.557G>A) pathogenic?

WDR62 p.Trp186Ter (c.557G>A) is classified Pathogenic in WDR62 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-04). No allele count reported in gnomAD v4.1 (AN 1,598,584).

How common is WDR62 p.Trp186Ter (c.557G>A) in the general population?

WDR62 p.Trp186Ter (c.557G>A) is no allele count reported in gnomAD v4.1 (AN 1,598,584) (gnomAD).

WDR62 p.Trp186Ter

c.557G>A · rs2513442799 · VCV2053008

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,598,584)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 5 of 32
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.4, phastCons 1
Overall
CADD	40.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,598,584). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: WDR62
Protein: p.Trp186Ter
Coding: c.557G>A
MANE Select: NM_001083961
dbSNP: rs2513442799
Type: single nucleotide variant
Location: chr19:36066423 (GRCh38)
Gene constraint: LOEUF 0.806 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 61.19

Full WDR62 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

WDR62 c.1234-1G>A Pathogenic/Likely pathogenic ★★ same type
WDR62 c.177+1G>C Pathogenic/Likely pathogenic ★★ same type
WDR62 c.2333+2T>C Likely pathogenic ★★ same type
WDR62 c.2520+5G>T Pathogenic ★★ same type
WDR62 c.269+1G>T Likely pathogenic ★★ same type
WDR62 c.3462+1G>A Pathogenic/Likely pathogenic ★★ same type
WDR62 c.3462+1G>C Pathogenic/Likely pathogenic ★★ same type
WDR62 c.3514+1G>A Pathogenic/Likely pathogenic ★★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/wdr62-p-trp186ter (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown