EMP2 p.Thr46=
c.138G>A · rs150309316 · VCV2202929
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0866%, 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 -8.3 | GERP -3.2 |
| Overall | ||
| CADD | 0.244 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0866%
African / African-American · 65/75,060 alleles
Filtering AF
0.0697%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0635%
Overall
0.00731%
118/1,614,214 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0866% | 1,155 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,946 |
| Admixed American | 0.0133% | 7,504 |
| European (non-Finnish) | 0.0028% | 35,758 |
| South Asian | 0.0011% | 91,086 |
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.Thr46=
- Coding
- c.138G>A
- MANE Select
- NM_001424
- dbSNP
- rs150309316
- Type
- single nucleotide variant
- Location
- chr16:10543601 (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-thr46 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown