Is ATRAID p.Gly107Ser (c.319G>A) pathogenic?

ATRAID p.Gly107Ser (c.319G>A) is classified Uncertain significance in ATRAID (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-23). AlphaMissense: likely benign (0.0938); Rare (popmax 0.115%, mid).

How common is ATRAID p.Gly107Ser (c.319G>A) in the general population?

ATRAID p.Gly107Ser (c.319G>A) is rare (popmax 0.115%, mid) (gnomAD).

What do computational predictors say about ATRAID p.Gly107Ser (c.319G>A)?

AlphaMissense predicts likely benign (score 0.0938) — an in-silico prediction, not a clinical call.

ATRAID p.Gly107Ser

c.319G>A · rs147492156 · VCV2455897

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0938 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.115%, mid)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0938	likely benign
REVEL	0.016	strongly benign-leaning
SaProt	LLR -10.49	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.1	GERP -2.3, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 4,576 bp · p 0.19 · regional, not allelic
Overall
CADD	15.14	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

Grpmax group 0.115% Middle Eastern · 7/6,084 alleles

Filtering AF 0.054% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0383%

Overall 0.00198% 32/1,614,080 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.115%	869
Remaining individualsnot grpmax-eligible	0.0064%	15,622
South Asian	0.0022%	45,547
Admixed American	0.00167%	60,008
European (non-Finnish)	0.00153%	65,558

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: ATRAID
Protein: p.Gly107Ser
Coding: c.319G>A
MANE Select: NM_001170795
dbSNP: rs147492156
Type: single nucleotide variant
Location: chr2:27215499 (GRCh38)
Gene constraint: LOEUF 1.235 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.31

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

Similar variants

ATRAID c.-117C>A Uncertain significance ★ same type
ATRAID c.-123A>C Uncertain significance ★ same type
ATRAID c.-155G>A Uncertain significance ★ same type
ATRAID c.-161A>G Uncertain significance ★ same type
ATRAID c.-24A>T Uncertain significance ★ same type
ATRAID c.-38C>T Uncertain significance ★ same type
ATRAID c.-44C>G Uncertain significance ★ same type
ATRAID c.-71G>A 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/atraid-p-gly107ser (accessed [today's date]).

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