Is EBP p.Ala139Pro (c.415G>C) pathogenic?

EBP p.Ala139Pro (c.415G>C) is classified Uncertain significance in EBP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-10). AlphaMissense: likely pathogenic (0.7774); Absent from gnomAD v4.1.

How common is EBP p.Ala139Pro (c.415G>C) in the general population?

EBP p.Ala139Pro (c.415G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EBP p.Ala139Pro (c.415G>C)?

AlphaMissense predicts likely pathogenic (score 0.7774) — an in-silico prediction, not a clinical call.

EBP p.Ala139Pro

c.415G>C · rs147961959 · VCV2853905

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7774 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.7774	likely pathogenic · top 8% in EBP
REVEL	0.839	moderately pathogenic-leaning
SaProt	LLR -15.35	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 2.1, phastCons 1
Overall
CADD	25.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

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.Ala139Pro
Coding: c.415G>C
MANE Select: NM_001378122 · reported on NM_006579
dbSNP: rs147961959
Type: single nucleotide variant
Location: chrX:48527231 (GRCh38)
Structure: AlphaFold pLDDT 59.09
Residue 139: the 'disordered' region

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

Similar variants

EBP p.Ala139Thr Uncertain significance ★ ⚠ same residue
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

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-ala139pro (accessed [today's date]).

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