Is EBP p.His9= (c.27C>T) pathogenic?

EBP p.His9= (c.27C>T) is classified Likely benign in EBP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-03). Very rare (popmax 0.00179%, afr).

How common is EBP p.His9= (c.27C>T) in the general population?

EBP p.His9= (c.27C>T) is very rare (popmax 0.00179%, afr) (gnomAD).

EBP p.His9=

c.27C>T · VCV4728385

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00179%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.56	GERP -2.2, phastCons 0.021
Overall
CADD	8.142	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00179% African / African-American · 1/55,721 alleles

Overall 0.000166% 2/1,203,808 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00179%	55,721
South Asian	0.00178%	56,241

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.His9=
Coding: c.27C>T
MANE Select: NM_001378122 · reported on NM_006579
Type: single nucleotide variant
Location: chrX:48523798 (GRCh38)
Structure: AlphaFold pLDDT 59.09

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

Similar variants

EBP p.His9Asp Uncertain significance ★ ⚠ same residue
EBP p.His9Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
EBP p.His9Tyr 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

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-his9 (accessed [today's date]).

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