Is EAF1 p.Thr4Ala (c.10A>G) pathogenic?

EAF1 p.Thr4Ala (c.10A>G) is classified Uncertain significance in EAF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-27). AlphaMissense: likely benign (0.0628); Very rare (popmax 0.00274%, afr).

How common is EAF1 p.Thr4Ala (c.10A>G) in the general population?

EAF1 p.Thr4Ala (c.10A>G) is very rare (popmax 0.00274%, afr) (gnomAD).

What do computational predictors say about EAF1 p.Thr4Ala (c.10A>G)?

AlphaMissense predicts likely benign (score 0.0628) — an in-silico prediction, not a clinical call.

EAF1 p.Thr4Ala

c.10A>G · VCV3843212

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0628 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00274%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0628	likely benign
REVEL	0.079	moderately benign-leaning
SaProt	LLR -6.29	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9	GERP 2.1, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 11 kb · p 3.8e-05 · regional, not allelic
Overall
CADD	19.53	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00274% African / African-American · 2/72,978 alleles

Filtering AF 0.000558% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000441%

Overall 0.000903% 14/1,551,030 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00274%	36,489
European (non-Finnish)	0.00105%	95,569

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: EAF1
Protein: p.Thr4Ala
Coding: c.10A>G
MANE Select: NM_033083
Type: single nucleotide variant
Location: chr3:15427789 (GRCh38)
Gene constraint: LOEUF 1.012 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.79 · 2 PDB

Full EAF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EAF1 p.Asp206= Benign ★★ same type
EAF1 p.Thr133= Benign ★★ same type
EAF1 p.Ala147Ser Uncertain significance ★ ⚠ same type
EAF1 p.Arg122Gln Uncertain significance ★ ⚠ same type
EAF1 p.Arg233Met Uncertain significance ★ ⚠ same type
EAF1 p.Arg233Thr Uncertain significance ★ ⚠ same type
EAF1 p.Arg27Gln Uncertain significance ★ ⚠ same type
EAF1 p.Asn216Ser 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/eaf1-p-thr4ala (accessed [today's date]).

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