Is CKAP5 p.Phe98Leu (c.294C>A) pathogenic?

CKAP5 p.Phe98Leu (c.294C>A) is classified Uncertain significance in CKAP5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-14). AlphaMissense: likely pathogenic (0.8326); Absent from gnomAD v4.1.

How common is CKAP5 p.Phe98Leu (c.294C>A) in the general population?

CKAP5 p.Phe98Leu (c.294C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CKAP5 p.Phe98Leu (c.294C>A)?

AlphaMissense predicts likely pathogenic (score 0.8326) — an in-silico prediction, not a clinical call.

CKAP5 p.Phe98Leu

c.294C>A · VCV4229268

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8326 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,900)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8326	likely pathogenic
REVEL	0.224	benign-leaning
SaProt	LLR -4.32	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.5	GERP 1.8, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 12 kb · p 0.39 · regional, not allelic
Overall
CADD	22.9	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

No allele count reported in gnomAD v4.1 (AN 1,613,900). 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: CKAP5
Protein: p.Phe98Leu
Coding: c.294C>A
MANE Select: NM_001008938
Type: single nucleotide variant
Location: chr11:46816362 (GRCh38)
Gene constraint: LOEUF 0.143 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.04 · 3 PDB
Residue 98: the 'tog 1' region

Full CKAP5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CKAP5 c.4569-2A>G Uncertain significance ★ same type
CKAP5 p.Ala1041Thr Uncertain significance ★ ⚠ same type
CKAP5 p.Ala1099Thr Uncertain significance ★ ⚠ same type
CKAP5 p.Ala1127Thr Uncertain significance ★ ⚠ same type
CKAP5 p.Ala124Ser Uncertain significance ★ ⚠ same type
CKAP5 p.Ala124Thr Uncertain significance ★ ⚠ same type
CKAP5 p.Ala1386Ser Uncertain significance ★ ⚠ same type
CKAP5 p.Ala1429Gly Uncertain significance ★ ⚠ 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/ckap5-p-phe98leu (accessed [today's date]).

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