Is WDR62 p.Asp955fs (c.2864_2867del) pathogenic?

WDR62 p.Asp955fs (c.28642867del) is classified Pathogenic in WDR62 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-11-11). Very rare (popmax 0.00373%, nfe); Associated with WDR62-related disorder.

What condition is associated with WDR62 p.Asp955fs (c.2864_2867del)?

WDR62 p.Asp955fs (c.2864_2867del) is associated with WDR62-related disorder (ClinVar).

How common is WDR62 p.Asp955fs (c.2864_2867del) in the general population?

WDR62 p.Asp955fs (c.2864_2867del) is very rare (popmax 0.00373%, nfe) (gnomAD).

WDR62 p.Asp955fs

c.2864_2867del · rs757827840 · VCV1362663

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00373%, nfe)

Conditions

WDR62-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 23 of 32
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.19	GERP -4.8, phastCons 0.13
Overall
CADD	24.5	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

Grpmax group 0.00373% European (non-Finnish) · 44/1,180,032 alleles

Filtering AF 0.00283% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00252%

Overall 0.00279% 45/1,614,064 alleles · very rare exomes 42/1,461,836 · genomes 3/152,228 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00373%	26,819
Remaining individualsnot grpmax-eligible	0.0016%	62,490

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: WDR62
Protein: p.Asp955fs
Coding: c.2864_2867del
MANE Select: NM_001083961
dbSNP: rs757827840
Type: Microsatellite
Location: chr19:36100867 (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

Disease context

WDR62-related disorder

Similar variants

WDR62 p.Asp955Asn Uncertain significance ★ ⚠ same residue
WDR62 p.Asp955Gly Uncertain significance ★ ⚠ same residue
WDR62 c.2520+5G>T Pathogenic ★★ same condition
WDR62 p.Asp511Asn Pathogenic/Likely pathogenic ★★ ⚠ same condition
WDR62 p.His381Asn Likely pathogenic ★★ ⚠ same condition
WDR62 c.178-2A>G Likely pathogenic ★ same condition
WDR62 c.1958+1G>A Likely pathogenic ★ same condition
WDR62 c.2467+1G>T Likely pathogenic ★ same condition

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-asp955fs (accessed [today's date]).

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