Is CDK5RAP2 p.Lys656Asn (c.1968G>C) pathogenic?

CDK5RAP2 p.Lys656Asn (c.1968G>C) is classified Likely pathogenic in CDK5RAP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-08-01). AlphaMissense: likely pathogenic (0.6134); Absent from gnomAD v4.1; Associated with microcephaly 3, primary, autosomal recessive.

What condition is associated with CDK5RAP2 p.Lys656Asn (c.1968G>C)?

CDK5RAP2 p.Lys656Asn (c.1968G>C) is associated with microcephaly 3, primary, autosomal recessive (ClinVar).

How common is CDK5RAP2 p.Lys656Asn (c.1968G>C) in the general population?

CDK5RAP2 p.Lys656Asn (c.1968G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDK5RAP2 p.Lys656Asn (c.1968G>C)?

AlphaMissense predicts likely pathogenic (score 0.6134) — an in-silico prediction, not a clinical call.

CDK5RAP2 p.Lys656Asn

c.1968G>C · VCV3336692

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6134 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

microcephaly 3, primary, autosomal recessive

Computational evidence

Protein change
AlphaMissense	0.6134	likely pathogenic ✓ concordant with ClinVar · top 6% in CDK5RAP2
REVEL	0.138	moderately benign-leaning
SaProt	LLR -8.39	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	Δ0.84	donor loss at this position · masked 0 · deltas
Pangolin	Δ0.78	loss · gain 0.01 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 5.9	GERP 2.1, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 191 kb · p 0.44 · regional, not allelic
Overall
CADD	34.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CDK5RAP2
Protein: p.Lys656Asn
Coding: c.1968G>C
MANE Select: NM_018249
Type: single nucleotide variant
Location: chr9:120470111 (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 c.4005-1G>A Pathogenic ★★ same condition
CDK5RAP2 c.4963+1G>A Likely pathogenic ★★ same condition
CDK5RAP2 p.Arg1403Ter Pathogenic/Likely pathogenic ★★ same condition
CDK5RAP2 p.Arg1481Ter Pathogenic/Likely pathogenic ★★ same condition
CDK5RAP2 p.Arg1558Ter Pathogenic ★★ same condition
CDK5RAP2 p.Arg427Ter Pathogenic ★★ same condition
CDK5RAP2 p.Gln1743Ter Pathogenic ★★ same condition
CDK5RAP2 p.Glu1516Ter 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-lys656asn (accessed [today's date]).

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