Is EBP p.Gln94His (c.282A>C) pathogenic?

EBP p.Gln94His (c.282A>C) is classified Benign/Likely benign in EBP (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-01). AlphaMissense: ambiguous (0.3499); Rare (popmax 0.592%, eas).

How common is EBP p.Gln94His (c.282A>C) in the general population?

EBP p.Gln94His (c.282A>C) is rare (popmax 0.592%, eas) (gnomAD).

What do computational predictors say about EBP p.Gln94His (c.282A>C)?

AlphaMissense predicts ambiguous (score 0.3499) — an in-silico prediction, not a clinical call.

EBP p.Gln94His

c.282A>C · rs182712356 · VCV764242

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

ambiguous

0.3499 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.592%, eas)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.3499	ambiguous
REVEL	0.664	pathogenic-leaning
SaProt	LLR -8.48	tolerated
⇒ REVEL calls this damaging; SaProt does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.6	GERP 1, phastCons 1
Overall
CADD	23.5	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 0.592% East Asian · 200/33,784 alleles

Filtering AF 0.525% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.499%

Overall 0.0197% 238/1,209,640 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.592%	169
Remaining individualsnot grpmax-eligible	0.0693%	1,443
South Asian	0.00176%	56,776
European (non-Finnish)	0.000447%	223,769

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.Gln94His
Coding: c.282A>C
MANE Select: NM_001378122 · reported on NM_006579
dbSNP: rs182712356
Type: single nucleotide variant
Location: chrX:48524053 (GRCh38)
Structure: AlphaFold pLDDT 59.09
Residue 94: 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-gln94his (accessed [today's date]).

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