Is CEACAM6 p.Val13Ile (c.37G>A) pathogenic?

CEACAM6 p.Val13Ile (c.37G>A) is classified Uncertain significance in CEACAM6 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-02). AlphaMissense: likely benign (0.0703); Absent from gnomAD v4.1.

How common is CEACAM6 p.Val13Ile (c.37G>A) in the general population?

CEACAM6 p.Val13Ile (c.37G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CEACAM6 p.Val13Ile (c.37G>A)?

AlphaMissense predicts likely benign (score 0.0703) — an in-silico prediction, not a clinical call.

CEACAM6 p.Val13Ile

c.37G>A · VCV4225006

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0703 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0703	likely benign
REVEL	0.003	strongly benign-leaning
SaProt	LLR -6.62	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 -12
Regional constraint	o/e 0.94	unconstrained · MANE · 11 kb · p 0.21 · regional, not allelic
Overall
CADD	0.003	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CEACAM6
Protein: p.Val13Ile
Coding: c.37G>A
MANE Select: NM_002483
Type: single nucleotide variant
Location: chr19:41755675 (GRCh38)
Gene constraint: LOEUF 0.908 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.52 · 6 PDB

Full CEACAM6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEACAM6 p.Gly85Glu Benign ★★ same type
CEACAM6 p.His260= Benign ★★ same type
CEACAM6 p.Ala105Thr Uncertain significance ★ ⚠ same type
CEACAM6 p.Ala134Val Uncertain significance ★ ⚠ same type
CEACAM6 p.Arg225His Uncertain significance ★ ⚠ same type
CEACAM6 p.Arg250Cys Uncertain significance ★ ⚠ same type
CEACAM6 p.Arg250His Uncertain significance ★ ⚠ same type
CEACAM6 p.Arg340Met 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/ceacam6-p-val13ile (accessed [today's date]).

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