Is CCNJL p.Ala292Val (c.875C>T) pathogenic?

CCNJL p.Ala292Val (c.875C>T) is classified Uncertain significance in CCNJL (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-08). AlphaMissense: likely benign (0.0774); Very rare (popmax 0.00802%, afr).

How common is CCNJL p.Ala292Val (c.875C>T) in the general population?

CCNJL p.Ala292Val (c.875C>T) is very rare (popmax 0.00802%, afr) (gnomAD).

What do computational predictors say about CCNJL p.Ala292Val (c.875C>T)?

AlphaMissense predicts likely benign (score 0.0774) — an in-silico prediction, not a clinical call.

CCNJL p.Ala292Val

c.875C>T · rs757655932 · VCV2323801

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0774 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00802%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0774	likely benign
REVEL	0.072	moderately benign-leaning
SaProt	LLR -6.41	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 4.2	GERP -1.3, phastCons 0.98
Regional constraint	o/e 1.02	unconstrained · MANE · 59 kb · p 0.58 · regional, not allelic
Overall
CADD	13.07	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 A340V vs ClinVar A292V) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00802% African / African-American · 6/74,838 alleles

Filtering AF 0.00347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00229%

Overall 0.00137% 22/1,608,642 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00802%	12,473
South Asian	0.00662%	15,114
East Asian	0.00224%	44,730
European (non-Finnish)	0.000765%	130,725

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.Ala292Val
Coding: c.875C>T
MANE Select: NM_001308173
dbSNP: rs757655932
Type: single nucleotide variant
Location: chr5:160253667 (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.Ala292Gly Uncertain significance ★ ⚠ same residue
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.Ala356Val Uncertain significance ★ ⚠ same type
CCNJL p.Ala366Thr Uncertain significance ★ ⚠ same type
CCNJL p.Arg175Cys 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-ala292val (accessed [today's date]).

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