EMP2 p.Thr153=
c.459C>A · rs1370457855 · VCV3060612
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00169%, amr)
Conditions
1
EMP2-related disorder
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 1.1 | GERP 0.71, phastCons 1 |
| Overall | ||
| CADD | 8.096 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00169%
Admixed American · 1/59,018 alleles
Filtering AF
0.000545%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00043%
Overall
0.00081%
13/1,604,636 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00169% | 59,018 |
| European (non-Finnish) | 0.00102% | 97,927 |
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.Thr153=
- Coding
- c.459C>A
- MANE Select
- NM_001424
- dbSNP
- rs1370457855
- Type
- single nucleotide variant
- Location
- chr16:10532950 (GRCh38)
- Gene constraint
- LOEUF 1.855 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.89
Disease context
EMP2-related disorder
Similar variants
- EMP2 c.*9A>G Likely benign same condition
- EMP2 p.Ile73= Likely benign same condition
- EMP2 p.Thr98= Likely benign same condition
- 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
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-thr153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown