Is CEACAM3 p.Ser66Asn (c.197G>A) pathogenic?

CEACAM3 p.Ser66Asn (c.197G>A) is classified Likely benign in CEACAM3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-05). AlphaMissense: likely benign (0.1507); Absent from gnomAD v4.1.

How common is CEACAM3 p.Ser66Asn (c.197G>A) in the general population?

CEACAM3 p.Ser66Asn (c.197G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CEACAM3 p.Ser66Asn (c.197G>A)?

AlphaMissense predicts likely benign (score 0.1507) — an in-silico prediction, not a clinical call.

CEACAM3 p.Ser66Asn

c.197G>A · rs2122987743 · VCV2592921

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1507 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1507	likely benign
REVEL	0.044	moderately benign-leaning
SaProt	LLR -4.96	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 -20	GERP -3.4
Regional constraint	o/e 0.92	unconstrained · MANE · 15 kb · p 0.14 · regional, not allelic
Overall
CADD	0.001	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

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: CEACAM3
Protein: p.Ser66Asn
Coding: c.197G>A
MANE Select: NM_001815
dbSNP: rs2122987743
Type: single nucleotide variant
Location: chr19:41797721 (GRCh38)
Gene constraint: LOEUF 1.359 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.52 · 4 PDB
Residue 66: a β-strand; the ig-like v-type domain

Full CEACAM3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEACAM3 p.Ala93Pro Benign ★★ same type
CEACAM3 p.Asn111= Likely benign ★★ same type
CEACAM3 p.Glu133Gly Benign ★★ ⚠ same type
CEACAM3 p.Leu78Gln Benign ★★ same type
CEACAM3 p.Ser77Arg Benign ★★ same type
CEACAM3 p.Thr103= Benign ★★ same type
CEACAM3 p.Thr135= Benign ★★ same type
CEACAM3 p.Tyr95Asn Benign ★★ 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/ceacam3-p-ser66asn (accessed [today's date]).

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