EMP1 p.Val11=
c.33C>T · rs2291061 · VCV2642743
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.604%, eas)
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 -0.19 | GERP 0.27, phastCons 0.27 |
| Overall | ||
| CADD | 7.379 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.604%
East Asian · 271/44,864 alleles
Filtering AF
0.545%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.522%
Overall
0.131%
2,108/1,612,748 alleles · rare
exomes 1,945/1,461,478 · genomes 163/151,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.604% | 166 |
| Admixed American | 0.391% | 256 |
| Middle Eastern | 0.28% | 357 |
| Remaining individualsnot grpmax-eligible | 0.146% | 687 |
| European (non-Finnish) | 0.121% | 824 |
| South Asian | 0.0385% | 2,598 |
| African / African-American | 0.0348% | 2,875 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,594 |
| Finnishnot grpmax-eligible | 0.00315% | 31,762 |
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
- EMP1
- Protein
- p.Val11=
- Coding
- c.33C>T
- MANE Select
- NM_001423
- dbSNP
- rs2291061
- Type
- single nucleotide variant
- Location
- chr12:13211543 (GRCh38)
- Gene constraint
- LOEUF 0.629 · pLI 0.82 (gnomAD)
- Structure
- AlphaFold pLDDT 90.68
Similar variants
- EMP1 p.Arg123Cys Uncertain significance ★ ⚠ same type
- EMP1 p.Arg123Ser Uncertain significance ★ ⚠ same type
- EMP1 p.Cys140Arg Uncertain significance ★ ⚠ same type
- EMP1 p.Cys142Ser Uncertain significance ★ same type
- EMP1 p.Gln127His Uncertain significance ★ ⚠ same type
- EMP1 p.Gly137Ser Uncertain significance ★ ⚠ same type
- EMP1 p.Gly92Arg Uncertain significance ★ ⚠ same type
- EMP1 p.Ile69Phe 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/emp1-p-val11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown