Is CCNJL p.Val103Ile (c.307G>A) pathogenic?

CCNJL p.Val103Ile (c.307G>A) is classified Benign in CCNJL (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-01). AlphaMissense: likely benign (0.1395); Low-frequency (popmax 1.21%, mid).

How common is CCNJL p.Val103Ile (c.307G>A) in the general population?

CCNJL p.Val103Ile (c.307G>A) is low-frequency (popmax 1.21%, mid) (gnomAD).

What do computational predictors say about CCNJL p.Val103Ile (c.307G>A)?

AlphaMissense predicts likely benign (score 0.1395) — an in-silico prediction, not a clinical call.

CCNJL p.Val103Ile

c.307G>A · rs139134014 · VCV2656010

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1395 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.21%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1395	likely benign
REVEL	0.246	benign-leaning
SaProt	LLR -5.43	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 4.9	GERP 1.4, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 59 kb · p 0.58 · regional, not allelic
Overall
CADD	23.1	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM V151I vs ClinVar V103I) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.21% Middle Eastern · 73/6,048 alleles

Filtering AF 1.15% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.14%

Overall 0.953% 15,350/1,611,468 alleles · low-frequency

Ancestry group	Frequency	1 in
Middle Easterngrpmax	1.21%	83
European (non-Finnish)	1.16%	86
Remaining individualsnot grpmax-eligible	0.892%	112
Admixed American	0.796%	126
Ashkenazi Jewishnot grpmax-eligible	0.557%	180
African / African-American	0.215%	466
South Asian	0.148%	678
Finnishnot grpmax-eligible	0.12%	831
East Asian	0.00446%	22,426

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.Val103Ile
Coding: c.307G>A
MANE Select: NM_001308173
dbSNP: rs139134014
Type: single nucleotide variant
Location: chr5:160259745 (GRCh38)
Gene constraint: LOEUF 1.263 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.40
Residue 103: the cyclin n-terminal domain

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-val103ile (accessed [today's date]).

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