Is CDK5RAP2 p.Glu340fs (c.1018del) pathogenic?

CDK5RAP2 p.Glu340fs (c.1018del) is classified Pathogenic in CDK5RAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2015-01-29). Absent from gnomAD; Associated with microcephaly 3, primary, autosomal recessive.

What condition is associated with CDK5RAP2 p.Glu340fs (c.1018del)?

CDK5RAP2 p.Glu340fs (c.1018del) is associated with microcephaly 3, primary, autosomal recessive (ClinVar).

How common is CDK5RAP2 p.Glu340fs (c.1018del) in the general population?

CDK5RAP2 p.Glu340fs (c.1018del) is absent from gnomAD (gnomAD).

CDK5RAP2 p.Glu340fs

c.1018del · rs797045441 · VCV210631

Pathogenic Single submitter

Classification

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 3, primary, autosomal recessive

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 11 of 38
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.4	GERP 1.5, phastCons 1

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: CDK5RAP2
Protein: p.Glu340fs
Coding: c.1018del
MANE Select: NM_018249
dbSNP: rs797045441
Type: Deletion
Location: chr9:120525060 (GRCh38)
Gene constraint: LOEUF 0.692 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 60.11 · 5 PDB

Full CDK5RAP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

microcephaly 3, primary, autosomal recessive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDK5RAP2 p.Gln175fs Pathogenic/Likely pathogenic ★★ same condition
CDK5RAP2 p.Leu1718fs Likely pathogenic ★★ same condition
CDK5RAP2 p.Met1326fs Likely pathogenic ★★ same condition
CDK5RAP2 p.Val1033fs Pathogenic ★★ same condition
CDK5RAP2 p.Asn459fs Pathogenic ★ same condition
CDK5RAP2 p.His1264fs Likely pathogenic ★ same condition
CDK5RAP2 p.Ile67fs Pathogenic ★ same condition
CDK5RAP2 p.Leu1006fs 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/cdk5rap2-p-glu340fs (accessed [today's date]).

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