Is CEACAM16 p.Val173= (c.519C>T) pathogenic?

CEACAM16 p.Val173= (c.519C>T) is classified Benign/Likely benign in CEACAM16 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-05-15). Rare (popmax 0.274%, afr).

How common is CEACAM16 p.Val173= (c.519C>T) in the general population?

CEACAM16 p.Val173= (c.519C>T) is rare (popmax 0.274%, afr) (gnomAD).

CEACAM16 p.Val173=

c.519C>T · rs114645388 · VCV227241

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.274%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -11	GERP -5.3
Overall
CADD	0.171	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.274% African / African-American · 204/74,346 alleles

Filtering AF 0.244% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.232%

Overall 0.0143% 227/1,589,278 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.274%	364
Remaining individualsnot grpmax-eligible	0.0163%	6,142
Admixed American	0.0158%	6,317
South Asian	0.00229%	43,733
European (non-Finnish)	0.000171%	584,488

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: CEACAM16
Protein: p.Val173=
Coding: c.519C>T
MANE Select: NM_001039213
dbSNP: rs114645388
Type: single nucleotide variant
Location: chr19:44704154 (GRCh38)
Gene constraint: LOEUF 1.139 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.50
Residue 173: the ig-like c2-type 1 domain; a disulfide bond

Full CEACAM16 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEACAM16 p.Val173Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
CEACAM16 c.1267+1G>A Uncertain significance ★★ same type
CEACAM16 p.Ala198Thr Uncertain significance ★★ ⚠ same type
CEACAM16 p.Ala355Thr Uncertain significance ★★ ⚠ same type
CEACAM16 p.Ala372Thr Uncertain significance ★★ ⚠ same type
CEACAM16 p.Ala375Val Uncertain significance ★★ ⚠ same type
CEACAM16 p.Ala50Thr Uncertain significance ★★ ⚠ same type
CEACAM16 p.Arg145Cys 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/ceacam16-p-val173 (accessed [today's date]).

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