Is WDR62 p.Ser1237fs (c.3711_3714del) pathogenic?

WDR62 p.Ser1237fs (c.37113714del) is classified Likely pathogenic in WDR62 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-06). No gnomAD frequency available for this variant; Associated with microcephaly 2, primary, autosomal recessive, with or without cortical malformations.

What condition is associated with WDR62 p.Ser1237fs (c.3711_3714del)?

WDR62 p.Ser1237fs (c.3711_3714del) is associated with microcephaly 2, primary, autosomal recessive, with or without cortical malformations (ClinVar).

How common is WDR62 p.Ser1237fs (c.3711_3714del) in the general population?

WDR62 p.Ser1237fs (c.3711_3714del) is no gnomAD frequency available for this variant (gnomAD).

WDR62 p.Ser1237fs

c.3711_3714del · rs2513785351 · VCV2690780

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

microcephaly 2, primary, autosomal recessive, with or without cortical malformations

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 30 of 32
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.78	GERP -0.48, phastCons 0.43

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Ser1237fs
Coding: c.3711_3714del
MANE Select: NM_001083961
dbSNP: rs2513785351
Type: Deletion
Location: chr19:36103537 (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

microcephaly 2, primary, autosomal recessive, with or without cortical malformations — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

WDR62 p.Ser696fs Pathogenic ★★ same condition
WDR62 p.Thr1244fs Pathogenic ★★ same condition
WDR62 c.1233+1del Likely pathogenic ★ same condition
WDR62 c.270-15_287del Likely pathogenic ★ same condition
WDR62 c.2740_2743del Likely pathogenic ★ same condition
WDR62 p.Ala1157fs Pathogenic ★ same condition
WDR62 p.Ala865fs Likely pathogenic ★ same condition
WDR62 p.Cys300fs 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-ser1237fs (accessed [today's date]).

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