Is CCNI p.Lys317Arg (c.950A>G) pathogenic?

CCNI p.Lys317Arg (c.950A>G) is classified Uncertain significance in CCNI (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-22). AlphaMissense: likely benign (0.0718); Very rare (popmax 0.005%, nfe).

How common is CCNI p.Lys317Arg (c.950A>G) in the general population?

CCNI p.Lys317Arg (c.950A>G) is very rare (popmax 0.005%, nfe) (gnomAD).

What do computational predictors say about CCNI p.Lys317Arg (c.950A>G)?

AlphaMissense predicts likely benign (score 0.0718) — an in-silico prediction, not a clinical call.

CCNI p.Lys317Arg

c.950A>G · VCV3487441

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0718 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.005%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0718	likely benign
REVEL	0.06	moderately benign-leaning
SaProt	LLR -6.00	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	GERP 0.46, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 7,107 bp · p 0.93 · regional, not allelic
Overall
CADD	16.06	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.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% European (non-Finnish) · 59/1,180,018 alleles

Filtering AF 0.00394% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00361%

Overall 0.0039% 63/1,614,006 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.005%	20,000
Remaining individualsnot grpmax-eligible	0.0032%	31,245
South Asian	0.0022%	45,539

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: CCNI
Protein: p.Lys317Arg
Coding: c.950A>G
MANE Select: NM_006835
Type: single nucleotide variant
Location: chr4:77048403 (GRCh38)
Gene constraint: LOEUF 0.574 · pLI 0.90 (gnomAD)
Structure: AlphaFold pLDDT 72.93

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

Similar variants

CCNI p.Lys317Asn Uncertain significance ★ ⚠ same residue
CCNI p.Ala190Thr Uncertain significance ★ ⚠ same type
CCNI p.Arg240Gln Uncertain significance ★ ⚠ same type
CCNI p.Arg32Gln Uncertain significance ★ ⚠ same type
CCNI p.Arg32Trp Uncertain significance ★ ⚠ same type
CCNI p.Asn39His Uncertain significance ★ ⚠ same type
CCNI p.Asn60Ser Uncertain significance ★ ⚠ same type
CCNI p.Asn9Tyr 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/ccni-p-lys317arg (accessed [today's date]).

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