Is EBP p.Arg171Gly (c.511C>G) pathogenic?

EBP p.Arg171Gly (c.511C>G) is classified Uncertain significance in EBP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-27). AlphaMissense: likely benign (0.2256); Very rare (popmax 9.11e-05%).

How common is EBP p.Arg171Gly (c.511C>G) in the general population?

EBP p.Arg171Gly (c.511C>G) is very rare (popmax 9.11e-05%) (gnomAD).

What do computational predictors say about EBP p.Arg171Gly (c.511C>G)?

AlphaMissense predicts likely benign (score 0.2256) — an in-silico prediction, not a clinical call.

EBP p.Arg171Gly

c.511C>G · VCV4950389

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2256 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 9.11e-05%)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2256	likely benign
REVEL	0.535	indeterminate
SaProt	LLR -11.35	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.97	GERP -1.2
Overall
CADD	17.84	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

Grpmax group 9.11e-05%

Overall 9.11e-05% 1/1,097,870 alleles · very rare

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: EBP
Protein: p.Arg171Gly
Coding: c.511C>G
MANE Select: NM_001378122 · reported on NM_006579
Type: single nucleotide variant
Location: chrX:48528275 (GRCh38)
Structure: AlphaFold pLDDT 59.09
Residue 171: the 'disordered' region

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

Similar variants

EBP p.Arg171= Benign/Likely benign ★★ same residue
EBP p.Arg171His Benign/Likely benign ★★ ⚠ same residue
EBP p.Arg171Cys Conflicting classifications of pathogenicity ★ ⚠ 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

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-arg171gly (accessed [today's date]).

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