ERMP1 p.Val404=
c.1212G>A · rs115468892 · VCV776407
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.63%, afr)
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 0.11 | GERP -2.6, phastCons 0.93 |
| Overall | ||
| CADD | 6.675 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.63%
African / African-American · 1,967/74,844 alleles
Filtering AF
2.53%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.49%
Overall
0.134%
2,157/1,613,576 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.63% | 38 |
| Remaining individualsnot grpmax-eligible | 0.158% | 631 |
| Admixed American | 0.123% | 810 |
| Middle Eastern | 0.0495% | 2,021 |
| South Asian | 0.00329% | 30,353 |
| European (non-Finnish) | 0.000932% | 107,263 |
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.Val404=
- Coding
- c.1212G>A
- MANE Select
- NM_024896
- dbSNP
- rs115468892
- Type
- single nucleotide variant
- Location
- chr9:5811226 (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.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
- ERMP1 p.Ala202Thr 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-val404 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown