Is EBP p.Phe140Cys (c.419T>G) pathogenic?

EBP p.Phe140Cys (c.419T>G) is classified Uncertain significance in EBP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2018-09-16). AlphaMissense: ambiguous (0.54); Absent from gnomAD v4.1.

How common is EBP p.Phe140Cys (c.419T>G) in the general population?

EBP p.Phe140Cys (c.419T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EBP p.Phe140Cys (c.419T>G)?

AlphaMissense predicts ambiguous (score 0.54) — an in-silico prediction, not a clinical call.

EBP p.Phe140Cys

c.419T>G · rs1569479908 · VCV591740

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.54 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.54	ambiguous
REVEL	0.874	moderately pathogenic-leaning
SaProt	LLR -6.85	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 7.8	GERP 2.1, phastCons 1
Overall
CADD	26.2	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EBP
Protein: p.Phe140Cys
Coding: c.419T>G
MANE Select: NM_001378122 · reported on NM_006579
dbSNP: rs1569479908
Type: single nucleotide variant
Location: chrX:48527235 (GRCh38)
Structure: AlphaFold pLDDT 59.09
Residue 140: 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-phe140cys (accessed [today's date]).

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