Is EBP p.Gly157Ser (c.469G>A) pathogenic?

EBP p.Gly157Ser (c.469G>A) is classified Pathogenic in EBP (ClinVar, Single submitter, 1 submitter; last evaluated 2017-09-06). AlphaMissense: ambiguous (0.4672); Absent from gnomAD v4.1.

How common is EBP p.Gly157Ser (c.469G>A) in the general population?

EBP p.Gly157Ser (c.469G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EBP p.Gly157Ser (c.469G>A)?

AlphaMissense predicts ambiguous (score 0.4672) — an in-silico prediction, not a clinical call.

EBP p.Gly157Ser

c.469G>A · rs2061782205 · VCV988320

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4672 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.4672	ambiguous
REVEL	0.883	moderately pathogenic-leaning
SaProt	LLR -10.96	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	Δ0.78	donor gain · deltas
Pangolin	Δ0.84	gain · loss 0.84 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Overall
CADD	36.0	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: EBP
Protein: p.Gly157Ser
Coding: c.469G>A
MANE Select: NM_001378122 · reported on NM_006579
dbSNP: rs2061782205
Type: single nucleotide variant
Location: chrX:48527285 (GRCh38)
Structure: AlphaFold pLDDT 59.09
Residue 157: the 'disordered' region

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

Similar variants

EBP p.Arg110Gln Pathogenic/Likely pathogenic ★★ same type
EBP p.Arg110Ter Pathogenic ★★ same type
EBP p.Arg147Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
EBP p.Arg147His Pathogenic ★★ ⚠ same type
EBP p.Arg62Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
EBP p.Glu80Lys Pathogenic/Likely pathogenic ★★ same type
EBP p.Gly161Arg Likely pathogenic ★★ same type
EBP p.Ser98Phe Pathogenic/Likely pathogenic ★★ 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/ebp-p-gly157ser (accessed [today's date]).

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