Is ATE1 p.Phe3= (c.9C>T) pathogenic?

ATE1 p.Phe3= (c.9C>T) is classified Benign in ATE1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-12-05). Common (popmax 21.6%, amr) — too common for a highly-penetrant pathogenic allele; Associated with ATE1-related disorder.

What condition is associated with ATE1 p.Phe3= (c.9C>T)?

ATE1 p.Phe3= (c.9C>T) is associated with ATE1-related disorder (ClinVar).

ATE1 p.Phe3=

Q: How common is ATE1 p.Phe3= (c.9C>T) in the general population?

ATE1 p.Phe3= (c.9C>T) is common (popmax 21.6%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.9C>T · rs79570924 · VCV3061001

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 21.6%, amr) — too common for a highly-penetrant pathogenic allele

Conditions

ATE1-related disorder

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 0.61	GERP -1, phastCons 0.99
Overall
CADD	9.302	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 21.6% Admixed American · 11,907/55,076 alleles

Filtering AF 21.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 21.2%

Overall 9.04% 141,571/1,565,434 alleles · common

Ancestry group	Frequency	1 in
Admixed Americangrpmax	21.6%	5
African / African-American	10.4%	10
Remaining individualsnot grpmax-eligible	8.87%	11
South Asian	8.86%	11
European (non-Finnish)	8.57%	12
East Asian	8.42%	12
Middle Eastern	8.37%	12
Finnishnot grpmax-eligible	7.77%	13
Ashkenazi Jewishnot grpmax-eligible	5.56%	18
Amishnot grpmax-eligible	4.61%	22

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.Phe3=
Coding: c.9C>T
MANE Select: NM_001001976
dbSNP: rs79570924
Type: single nucleotide variant
Location: chr10:121927941 (GRCh38)
Gene constraint: LOEUF 0.687 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.56 · 2 PDB

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.Asp357= Likely benign same condition
ATE1 p.Leu101= 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-phe3 (accessed [today's date]).

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