Is EBP p.Tyr111= (c.333C>T) pathogenic?

EBP p.Tyr111= (c.333C>T) is classified Likely benign in EBP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-09-07). Very rare (popmax 0.00067%, nfe).

How common is EBP p.Tyr111= (c.333C>T) in the general population?

EBP p.Tyr111= (c.333C>T) is very rare (popmax 0.00067%, nfe) (gnomAD).

EBP p.Tyr111=

c.333C>T · rs2061781158 · VCV3026749

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00067%, nfe)

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 -1.1	GERP -1.1
Overall
CADD	3.632	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00067% European (non-Finnish) · 6/895,394 alleles

Filtering AF 0.000241% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000158%

Overall 0.001% 11/1,098,066 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.00852%	11,732
Remaining individualsnot grpmax-eligible	0.0021%	47,648
European (non-Finnish)grpmax	0.00067%	149,232

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Tyr111=
Coding: c.333C>T
MANE Select: NM_001378122 · reported on NM_006579
dbSNP: rs2061781158
Type: single nucleotide variant
Location: chrX:48527020 (GRCh38)
Structure: AlphaFold pLDDT 59.09
Residue 111: the 'disordered' region

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

Similar variants

EBP p.Tyr111Asn Likely pathogenic ★ same residue
EBP p.Tyr111His Likely pathogenic ★ same residue
EBP p.Tyr111Ter Pathogenic ★ 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-tyr111 (accessed [today's date]).

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