Is CDK5RAP2 p.Val47fs (c.140del) pathogenic?

CDK5RAP2 p.Val47fs (c.140del) is classified Likely pathogenic in CDK5RAP2 (ClinVar, Single submitter, 1 submitter). Absent from gnomAD.

How common is CDK5RAP2 p.Val47fs (c.140del) in the general population?

CDK5RAP2 p.Val47fs (c.140del) is absent from gnomAD (gnomAD).

CDK5RAP2 p.Val47fs

c.140del · rs786205660 · VCV191346

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

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 3 of 38
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.14	GERP -2.2, phastCons 0.36

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.Val47fs
Coding: c.140del
MANE Select: NM_018249
dbSNP: rs786205660
Type: Deletion
Location: chr9:120568376 (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

Similar variants

CDK5RAP2 p.Val47Xaa Pathogenic ★ same residue
CDK5RAP2 p.Gln175fs Pathogenic/Likely pathogenic ★★ same type
CDK5RAP2 p.Leu1718fs Likely pathogenic ★★ same type
CDK5RAP2 p.Met1326fs Likely pathogenic ★★ same type
CDK5RAP2 p.Val1033fs Pathogenic ★★ same type
CDK5RAP2 c.2107-15_2108del Likely pathogenic ★ same type
CDK5RAP2 c.4408_4414+15del Likely pathogenic ★ same type
CDK5RAP2 p.Asn1388fs 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/cdk5rap2-p-val47fs (accessed [today's date]).

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