Is EDRF1 p.Val1042Phe (c.3124G>T) pathogenic?

EDRF1 p.Val1042Phe (c.3124G>T) is classified Uncertain significance in EDRF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-29). AlphaMissense: ambiguous (0.5356); Absent from gnomAD v4.1.

How common is EDRF1 p.Val1042Phe (c.3124G>T) in the general population?

EDRF1 p.Val1042Phe (c.3124G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EDRF1 p.Val1042Phe (c.3124G>T)?

AlphaMissense predicts ambiguous (score 0.5356) — an in-silico prediction, not a clinical call.

EDRF1 p.Val1042Phe

c.3124G>T · rs2493675880 · VCV3087213

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5356 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.5356	ambiguous
REVEL	0.331	indeterminate
SaProt	LLR -7.50	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 0.77	unconstrained · MANE · 38 kb · p 3.4e-16 · regional, not allelic
Overall
CADD	34.0	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: EDRF1
Protein: p.Val1042Phe
Coding: c.3124G>T
MANE Select: NM_001202438
dbSNP: rs2493675880
Type: single nucleotide variant
Location: chr10:125749412 (GRCh38)
Gene constraint: LOEUF 0.53 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 76.41

Full EDRF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EDRF1 p.Leu159= Benign ★★ same type
EDRF1 p.Thr480= Benign ★★ same type
EDRF1 p.Thr731= Benign ★★ same type
EDRF1 p.Ala1137Ser Uncertain significance ★ ⚠ same type
EDRF1 p.Ala1210Thr Uncertain significance ★ ⚠ same type
EDRF1 p.Ala1228Thr Uncertain significance ★ ⚠ same type
EDRF1 p.Ala203Thr Uncertain significance ★ ⚠ same type
EDRF1 p.Ala226Ser 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/edrf1-p-val1042phe (accessed [today's date]).

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