Is CCNI2 p.Pro47Ser (c.139C>T) pathogenic?

CCNI2 p.Pro47Ser (c.139C>T) is classified Likely benign in CCNI2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-06). AlphaMissense: likely benign (0.0785); Absent from gnomAD v4.1.

How common is CCNI2 p.Pro47Ser (c.139C>T) in the general population?

CCNI2 p.Pro47Ser (c.139C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCNI2 p.Pro47Ser (c.139C>T)?

AlphaMissense predicts likely benign (score 0.0785) — an in-silico prediction, not a clinical call.

CCNI2 p.Pro47Ser

c.139C>T · rs1266485094 · VCV2254057

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0785 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,503,318)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0785	likely benign
REVEL	0.012	strongly benign-leaning
SaProt	LLR -6.87	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 -1.3	GERP -4.9
Regional constraint	o/e 0.93	unconstrained · MANE · 5,471 bp · p 0.12 · regional, not allelic
Overall
CADD	5.463	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

No allele count reported in gnomAD v4.1 (AN 1,503,318). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CCNI2
Protein: p.Pro47Ser
Coding: c.139C>T
MANE Select: NM_001039780
dbSNP: rs1266485094
Type: single nucleotide variant
Location: chr5:132747634 (GRCh38)
Gene constraint: LOEUF 1.451 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.87
Residue 47: the 'disordered' region

Full CCNI2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCNI2 p.Ala2Val Uncertain significance ★ ⚠ same type
CCNI2 p.Arg108Cys Uncertain significance ★ ⚠ same type
CCNI2 p.Arg159Trp Uncertain significance ★ ⚠ same type
CCNI2 p.Arg55Ser Uncertain significance ★ ⚠ same type
CCNI2 p.Arg77Gly Uncertain significance ★ ⚠ same type
CCNI2 p.Arg79Gly Uncertain significance ★ ⚠ same type
CCNI2 p.Asp116Asn Uncertain significance ★ ⚠ same type
CCNI2 p.Asp118Glu 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/ccni2-p-pro47ser (accessed [today's date]).

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