Is CCNJL p.Met267Val (c.799A>G) pathogenic?

CCNJL p.Met267Val (c.799A>G) is classified Uncertain significance in CCNJL (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-07). AlphaMissense: likely benign (0.0568); Very rare (popmax 0.00715%, sas).

How common is CCNJL p.Met267Val (c.799A>G) in the general population?

CCNJL p.Met267Val (c.799A>G) is very rare (popmax 0.00715%, sas) (gnomAD).

What do computational predictors say about CCNJL p.Met267Val (c.799A>G)?

AlphaMissense predicts likely benign (score 0.0568) — an in-silico prediction, not a clinical call.

CCNJL p.Met267Val

c.799A>G · rs752290089 · VCV3139964

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0568 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00715%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0568	likely benign
REVEL	0.045	moderately benign-leaning
SaProt	LLR -5.16	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.55	GERP -3.8
Regional constraint	o/e 1.02	unconstrained · MANE · 59 kb · p 0.58 · regional, not allelic
Overall
CADD	0.132	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM M315V vs ClinVar M267V) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00715% South Asian · 6/83,892 alleles

Filtering AF 0.00402% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00368%

Overall 0.00436% 68/1,561,190 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00715%	13,982
European (non-Finnish)	0.00511%	19,585
Remaining individualsnot grpmax-eligible	0.00331%	30,233
East Asian	0.00226%	44,276

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CCNJL
Protein: p.Met267Val
Coding: c.799A>G
MANE Select: NM_001308173
dbSNP: rs752290089
Type: single nucleotide variant
Location: chr5:160253743 (GRCh38)
Gene constraint: LOEUF 1.263 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.40

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

Similar variants

CCNJL p.Ala148Thr Uncertain significance ★ ⚠ same type
CCNJL p.Ala207Ser Uncertain significance ★ ⚠ same type
CCNJL p.Ala266Thr Uncertain significance ★ ⚠ same type
CCNJL p.Ala284Val Uncertain significance ★ ⚠ same type
CCNJL p.Ala292Gly Uncertain significance ★ ⚠ same type
CCNJL p.Ala292Val Uncertain significance ★ ⚠ same type
CCNJL p.Ala356Val Uncertain significance ★ ⚠ same type
CCNJL p.Ala366Thr 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/ccnjl-p-met267val (accessed [today's date]).

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