EBP p.Ser65Pro
c.193T>C · VCV3598329
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely benign
0.2502 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
AlphaMissense, SaProt · REVEL no call
Conditions
2
MEND syndrome
Computational evidence
| Protein change | ||
| AlphaMissense | 0.2502 | likely benign |
|---|---|---|
| REVEL | 0.598 | indeterminate |
| SaProt | LLR -10.19 | damaging |
| ⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.50 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 23.4 | 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.Ser65Pro
- Coding
- c.193T>C
- MANE Select
- NM_006579
- Type
- single nucleotide variant
- Location
- chrX:48523964 (GRCh38)
- Structure
- AlphaFold pLDDT 59.09
- Residue 65
- a modified residue (phosphoserine); the 'disordered' region
Similar variants
- EBP p.Ser65Phe Uncertain significance ★ ⚠ same residue
- EBP p.Arg110Gln Pathogenic/Likely pathogenic ★★ same condition
- EBP p.Arg110Ter Pathogenic ★★ same condition
- EBP p.Arg147Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- EBP p.Arg147His Pathogenic ★★ ⚠ same condition
- EBP p.Arg62Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
- EBP p.Glu80Lys Pathogenic/Likely pathogenic ★★ same condition
- EBP p.Gly161Arg Likely pathogenic ★★ 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-ser65pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown