Is EBP p.Thr217= (c.651G>A) pathogenic?

EBP p.Thr217= (c.651G>A) is classified Likely benign in EBP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-24). Ultra-rare (popmax 0.0107%, afr); Associated with Inborn genetic diseases.

What condition is associated with EBP p.Thr217= (c.651G>A)?

EBP p.Thr217= (c.651G>A) is associated with Inborn genetic diseases (ClinVar).

How common is EBP p.Thr217= (c.651G>A) in the general population?

EBP p.Thr217= (c.651G>A) is ultra-rare (popmax 0.0107%, afr) (gnomAD).

EBP p.Thr217=

c.651G>A · VCV4015967

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, afr)

Conditions

Inborn genetic diseases

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 -0.046	GERP -4.2
Overall
CADD	0.612	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0107% African / African-American · 6/56,061 alleles

Filtering AF 0.00464% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00312%

Overall 0.00102% 12/1,173,009 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0107%	9,344
Remaining individualsnot grpmax-eligible	0.00217%	46,160
South Asian	0.00189%	52,903
European (non-Finnish)	0.000457%	219,049

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.Thr217=
Coding: c.651G>A
MANE Select: NM_001378122 · reported on NM_006579
Type: single nucleotide variant
Location: chrX:48528415 (GRCh38)
Structure: AlphaFold pLDDT 59.09

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EBP p.Thr217Met Benign/Likely benign ★★ same residue
EBP p.Gly173Arg Uncertain significance ★★ ⚠ same condition
EBP p.Gly177Arg Uncertain significance ★★ ⚠ same condition
EBP p.Arg171His Benign/Likely benign ★★ ⚠ same condition
EBP p.Arg52Cys Benign/Likely benign ★★ ⚠ same condition
EBP c.301+3G>C Conflicting classifications of pathogenicity ★ same condition
EBP p.Arg142His Uncertain significance ★ ⚠ same condition
EBP p.Asn4Ile Uncertain significance ★ ⚠ same condition

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-thr217 (accessed [today's date]).

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