Is ATE1 p.Asp357= (c.1071C>T) pathogenic?

ATE1 p.Asp357= (c.1071C>T) is classified Likely benign in ATE1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-12). Ultra-rare (popmax 0.0121%, afr); Associated with ATE1-related disorder.

What condition is associated with ATE1 p.Asp357= (c.1071C>T)?

ATE1 p.Asp357= (c.1071C>T) is associated with ATE1-related disorder (ClinVar).

How common is ATE1 p.Asp357= (c.1071C>T) in the general population?

ATE1 p.Asp357= (c.1071C>T) is ultra-rare (popmax 0.0121%, afr) (gnomAD).

ATE1 p.Asp357=

c.1071C>T · rs751448391 · VCV3058116

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0121%, afr)

Conditions

ATE1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.186	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.4	GERP 0.6, phastCons 1
Overall
CADD	8.778	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0121% African / African-American · 9/74,610 alleles

Filtering AF 0.00626% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00469%

Overall 0.000749% 12/1,602,180 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0121%	8,290
Remaining individualsnot grpmax-eligible	0.00323%	30,915
Admixed American	0.00168%	59,664

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: ATE1
Protein: p.Asp357=
Coding: c.1071C>T
MANE Select: NM_001001976
dbSNP: rs751448391
Type: single nucleotide variant
Location: chr10:121841168 (GRCh38)
Gene constraint: LOEUF 0.687 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.56 · 2 PDB
Residue 357: a β-strand

Full ATE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ATE1-related disorder

Similar variants

ATE1 c.1157+7T>C Benign same condition
ATE1 c.942+1004C>T Likely benign same condition
ATE1 c.*8A>G Benign same condition
ATE1 p.Ala123= Likely benign same condition
ATE1 p.Leu101= Benign same condition
ATE1 p.Phe3= Benign same condition
ATE1 p.Pro457= Benign same condition
ATE1 p.Ser412= Benign 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/ate1-p-asp357 (accessed [today's date]).

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