EMP2 p.Thr23=
c.69C>T · VCV4681567
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, 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 5.7 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 8.191 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,876 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000971%
Overall
0.0018%
29/1,613,960 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,438 |
| South Asian | 0.00439% | 22,767 |
| European (non-Finnish) | 0.00178% | 56,191 |
| Finnishnot grpmax-eligible | 0.00156% | 64,020 |
| African / African-American | 0.00133% | 74,920 |
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.Thr23=
- Coding
- c.69C>T
- MANE Select
- NM_001424
- Type
- single nucleotide variant
- Location
- chr16:10547549 (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-thr23 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown