Is CCNI p.Asp117Val (c.350A>T) pathogenic?

CCNI p.Asp117Val (c.350A>T) is classified Uncertain significance in CCNI (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-13). AlphaMissense: likely pathogenic (0.5996); Very rare (popmax 0.00892%, eas).

How common is CCNI p.Asp117Val (c.350A>T) in the general population?

CCNI p.Asp117Val (c.350A>T) is very rare (popmax 0.00892%, eas) (gnomAD).

What do computational predictors say about CCNI p.Asp117Val (c.350A>T)?

AlphaMissense predicts likely pathogenic (score 0.5996) — an in-silico prediction, not a clinical call.

CCNI p.Asp117Val

c.350A>T · VCV4222119

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5996 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00892%, eas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.5996	likely pathogenic
REVEL	0.14	moderately benign-leaning
SaProt	LLR -9.04	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 7.9	GERP 1.9, phastCons 1
Regional constraint	o/e 0.70	unconstrained · MANE · 11 kb · p 4.1e-05 · regional, not allelic
Overall
CADD	23.0	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

Grpmax group 0.00892% East Asian · 4/44,830 alleles

Filtering AF 0.00298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0018%

Overall 0.000274% 4/1,461,494 alleles · very rare

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.Asp117Val
Coding: c.350A>T
MANE Select: NM_006835
Type: single nucleotide variant
Location: chr4:77056071 (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.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
CCNI p.Gln193His 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-asp117val (accessed [today's date]).

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