Is CEACAM16 p.Asp333= (c.999C>T) pathogenic?

CEACAM16 p.Asp333= (c.999C>T) is classified Benign/Likely benign in CEACAM16 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-18). Rare (popmax 0.139%, nfe).

How common is CEACAM16 p.Asp333= (c.999C>T) in the general population?

CEACAM16 p.Asp333= (c.999C>T) is rare (popmax 0.139%, nfe) (gnomAD).

CEACAM16 p.Asp333=

c.999C>T · rs200767877 · VCV504818

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.139%, nfe)

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 -6.4	GERP -5.5
Overall
CADD	8.361	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.139% European (non-Finnish) · 1,613/1,160,610 alleles

Filtering AF 0.133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.131%

Overall 0.116% 1,845/1,586,864 alleles · rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.159%	630
Finnishnot grpmax-eligible	0.15%	667
European (non-Finnish)grpmax	0.139%	720
Admixed American	0.0425%	2,356
African / African-American	0.0214%	4,663

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Asp333=
Coding: c.999C>T
MANE Select: NM_001039213
dbSNP: rs200767877
Type: single nucleotide variant
Location: chr19:44707919 (GRCh38)
Gene constraint: LOEUF 1.139 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.50

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

Similar variants

CEACAM16 p.Asp333Glu Uncertain significance ★ ⚠ 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-asp333 (accessed [today's date]).

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