Is CCDC144A p.Glu232= (c.696A>G) pathogenic?

CCDC144A p.Glu232= (c.696A>G) is classified Likely benign in CCDC144A (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-01). Rare (popmax 0.284%, amr).

How common is CCDC144A p.Glu232= (c.696A>G) in the general population?

CCDC144A p.Glu232= (c.696A>G) is rare (popmax 0.284%, amr) (gnomAD).

CCDC144A p.Glu232=

c.696A>G · rs534183012 · VCV3025424

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.284%, amr)

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 0.92
Overall
CADD	3.918	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.284% Admixed American · 168/59,244 alleles

Filtering AF 0.249% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.235%

Overall 0.0131% 211/1,607,132 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.284%	353
Remaining individualsnot grpmax-eligible	0.0354%	2,824
African / African-American	0.0214%	4,673
European (non-Finnish)	0.000424%	235,580

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: CCDC144A
Protein: p.Glu232=
Coding: c.696A>G
MANE Select: NM_001382000
dbSNP: rs534183012
Type: single nucleotide variant
Location: chr17:16707500 (GRCh38)
Gene constraint: LOEUF 0.57 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 61.65
Residue 232: the 'disordered' region

Full CCDC144A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC144A p.Ala1033Ser Uncertain significance ★ ⚠ same type
CCDC144A p.Ala1080Val Uncertain significance ★ ⚠ same type
CCDC144A p.Ala1121Ser Uncertain significance ★ ⚠ same type
CCDC144A p.Ala1195Thr Uncertain significance ★ ⚠ same type
CCDC144A p.Ala1206Ser Uncertain significance ★ ⚠ same type
CCDC144A p.Ala1206Val Uncertain significance ★ ⚠ same type
CCDC144A p.Ala1381Gly Uncertain significance ★ ⚠ same type
CCDC144A p.Ala1382= 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/ccdc144a-p-glu232 (accessed [today's date]).

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