EMP2 p.Phe82=
c.246C>T · rs375756110 · VCV2171015
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0223%, 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 0.27 | GERP -2.1, phastCons 0.002 |
| Overall | ||
| CADD | 9.311 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0223%
East Asian · 10/44,884 alleles
Filtering AF
0.012%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00916%
Overall
0.00198%
32/1,614,006 alleles · ultra-rare
exomes 27/1,461,872 · genomes 5/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0223% | 4,488 |
| South Asian | 0.00769% | 13,011 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| Admixed American | 0.00333% | 30,002 |
| African / African-American | 0.00133% | 74,910 |
| European (non-Finnish) | 0.000763% | 131,113 |
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
- EMP2
- Protein
- p.Phe82=
- Coding
- c.246C>T
- MANE Select
- NM_001424
- dbSNP
- rs375756110
- Type
- single nucleotide variant
- Location
- chr16:10537998 (GRCh38)
- Gene constraint
- LOEUF 1.855 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.89
Similar variants
- EMP2 p.Ala63Val Uncertain significance ★★ ⚠ same type
- EMP2 p.Ala78Thr Uncertain significance ★★ ⚠ same type
- EMP2 p.Arg120His Uncertain significance ★★ ⚠ same type
- EMP2 p.Arg166His Uncertain significance ★★ ⚠ same type
- EMP2 p.Glu121Lys Uncertain significance ★★ ⚠ same type
- EMP2 p.Ile69Met Uncertain significance ★★ ⚠ same type
- EMP2 p.Thr43Ile Uncertain significance ★★ ⚠ same type
- EMP2 p.Tyr143His 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/emp2-p-phe82 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown