Is ATAD1 p.Gln352Pro (c.1055A>C) pathogenic?

ATAD1 p.Gln352Pro (c.1055A>C) is classified Uncertain significance in ATAD1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-12-20). AlphaMissense: likely benign (0.0703); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ATAD1 p.Gln352Pro (c.1055A>C)?

ATAD1 p.Gln352Pro (c.1055A>C) is associated with Inborn genetic diseases (ClinVar).

How common is ATAD1 p.Gln352Pro (c.1055A>C) in the general population?

ATAD1 p.Gln352Pro (c.1055A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ATAD1 p.Gln352Pro (c.1055A>C)?

AlphaMissense predicts likely benign (score 0.0703) — an in-silico prediction, not a clinical call.

ATAD1 p.Gln352Pro

c.1055A>C · rs1564735515 · VCV1486458

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0703 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0703	likely benign
REVEL	0.46	indeterminate
SaProt	LLR -10.68	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 1.8, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 22 kb · p 0.014 · regional, not allelic
Overall
CADD	22.0	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ATAD1
Protein: p.Gln352Pro
Coding: c.1055A>C
MANE Select: NM_001321967
dbSNP: rs1564735515
Type: single nucleotide variant
Location: chr10:87754718 (GRCh38)
Gene constraint: LOEUF 0.505 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 84.05 · 2 PDB
Residue 352: a UniProt-annotated variant site (in hkpx4; severely decreased atad1 mrna expression in lymphoblastoid cells derived from the patient compared to an unaffected control)

Full ATAD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ATAD1 p.Gln352Arg Uncertain significance ★ ⚠ same residue
ATAD1 p.Ala339Val Uncertain significance ★★ ⚠ same condition
ATAD1 p.Ala55Thr Uncertain significance ★★ ⚠ same condition
ATAD1 p.Arg338Gln Uncertain significance ★★ ⚠ same condition
ATAD1 p.Asp164Asn Uncertain significance ★★ ⚠ same condition
ATAD1 p.Gln185Glu Uncertain significance ★★ ⚠ same condition
ATAD1 p.Glu290Lys Uncertain significance ★★ ⚠ same condition
ATAD1 p.His227Asn Uncertain significance ★★ ⚠ same condition

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/atad1-p-gln352pro (accessed [today's date]).

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