Is CLUAP1 p.Ala93= (c.279G>A) pathogenic?

CLUAP1 p.Ala93= (c.279G>A) is classified Likely benign in CLUAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-12). Ultra-rare (popmax 0.0189%, sas).

How common is CLUAP1 p.Ala93= (c.279G>A) in the general population?

CLUAP1 p.Ala93= (c.279G>A) is ultra-rare (popmax 0.0189%, sas) (gnomAD).

CLUAP1 p.Ala93=

c.279G>A · rs769586346 · VCV1627700

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0189%, sas)

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 -1	GERP -4
Overall
CADD	5.406	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0189% South Asian · 17/89,924 alleles

Filtering AF 0.012% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00988%

Overall 0.0028% 45/1,609,616 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0189%	5,290
East Asian	0.00225%	44,532
European (non-Finnish)	0.00212%	47,154
Remaining individualsnot grpmax-eligible	0.0016%	62,342
African / African-American	0.00134%	74,536

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: CLUAP1
Protein: p.Ala93=
Coding: c.279G>A
MANE Select: NM_015041
dbSNP: rs769586346
Type: single nucleotide variant
Location: chr16:3508348 (GRCh38)
Gene constraint: LOEUF 1.23 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.02

Full CLUAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CLUAP1 p.Ala93Val Uncertain significance ★ ⚠ same residue
CLUAP1 p.Ala152Glu Uncertain significance ★★ ⚠ same type
CLUAP1 p.Ala188Gly Uncertain significance ★★ ⚠ same type
CLUAP1 p.Ala339Thr Uncertain significance ★★ ⚠ same type
CLUAP1 p.Arg20Gln Uncertain significance ★★ ⚠ same type
CLUAP1 p.Arg228Gln Uncertain significance ★★ ⚠ same type
CLUAP1 p.Arg304His Uncertain significance ★★ ⚠ same type
CLUAP1 p.Arg332Gln 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/cluap1-p-ala93 (accessed [today's date]).

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