ERMP1 p.Pro681=
c.2043G>A · rs775344090 · VCV3025207
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.3 | GERP -4.5 |
| Overall | ||
| CADD | 4.066 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,080 alleles
Filtering AF
0.00211%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00137%
Overall
0.000806%
13/1,612,250 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,080 |
| South Asian | 0.00552% | 18,116 |
| East Asian | 0.00223% | 44,794 |
| African / African-American | 0.00134% | 74,818 |
| European (non-Finnish) | 0.000424% | 235,871 |
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
- ERMP1
- Protein
- p.Pro681=
- Coding
- c.2043G>A
- MANE Select
- NM_024896
- dbSNP
- rs775344090
- Type
- single nucleotide variant
- Location
- chr9:5801200 (GRCh38)
- Gene constraint
- LOEUF 1.239 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.45
Similar variants
- ERMP1 c.1021+6T>C Likely benign ★★ same type
- ERMP1 p.Gly809= Benign ★★ same type
- ERMP1 p.Ser531= Benign ★★ same type
- ERMP1 p.Val404= Benign ★★ same type
- ERMP1 p.Ala109Gly Uncertain significance ★ ⚠ same type
- ERMP1 p.Ala109Val Uncertain significance ★ ⚠ same type
- ERMP1 p.Ala112Thr Uncertain significance ★ ⚠ same type
- ERMP1 p.Ala196Asp 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/ermp1-p-pro681 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown