ENTREP2 p.Ser367=
c.1101C>A · rs1273798522 · VCV2645095
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000175%, 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 -1.2 | GERP -2.3 |
| Overall | ||
| CADD | 0.267 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000175%
European (non-Finnish) · 2/1,145,930 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000143%
2/1,395,258 alleles · very rare
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
- ENTREP2
- Protein
- p.Ser367=
- Coding
- c.1101C>A
- MANE Select
- NM_015307
- dbSNP
- rs1273798522
- Type
- single nucleotide variant
- Location
- chr15:29126394 (GRCh38)
- Structure
- AlphaFold pLDDT 59.09
- Residue 367
- the 'disordered' region
Similar variants
- ENTREP2 p.Gly126Ser Uncertain significance ★★ ⚠ same type
- NSMCE3 p.Ala293Thr Uncertain significance ★★ ⚠ same type
- NSMCE3 p.Arg133Ser Uncertain significance ★★ ⚠ same type
- NSMCE3 p.Gln14His Uncertain significance ★★ ⚠ same type
- NSMCE3 p.Glu45Gln Uncertain significance ★★ ⚠ same type
- NSMCE3 p.Gly78Arg Uncertain significance ★★ ⚠ same type
- NSMCE3 p.Ile193Val Uncertain significance ★★ ⚠ same type
- NSMCE3 p.Pro65Leu Uncertain significance ★★ ⚠ 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/entrep2-p-ser367 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown