EME2 p.Ser317=
c.951C>T · rs143964421 · VCV787434
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.74%, 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 -4.3 | GERP -4.8 |
| Overall | ||
| CADD | 1.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.74%
African / African-American · 555/75,028 alleles
Filtering AF
0.689%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.669%
Overall
0.0421%
677/1,609,448 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.74% | 135 |
| Middle Eastern | 0.248% | 403 |
| Remaining individualsnot grpmax-eligible | 0.0609% | 1,641 |
| Admixed American | 0.0567% | 1,763 |
| European (non-Finnish) | 0.00288% | 34,681 |
| South Asian | 0.0011% | 90,950 |
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
- EME2
- Protein
- p.Ser317=
- Coding
- c.951C>T
- MANE Select
- NM_001257370
- dbSNP
- rs143964421
- Type
- single nucleotide variant
- Location
- chr16:1775968 (GRCh38)
- Gene constraint
- LOEUF 1.942 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.73 · 1 PDB
- Residue 317
- the 'helix-hairpin-helix (2hhh); forms the pre-nick dna binding interface and is involved in dna recognition and bending' region
Similar variants
- SPSB3 p.Leu317Pro Uncertain significance ★ ⚠ same residue
- MRPS34 p.Gln32Ter Pathogenic/Likely pathogenic ★★ same type
- MRPS34 p.Arg17Pro Uncertain significance ★★ ⚠ same type
- MRPS34 p.Arg27Lys Uncertain significance ★★ ⚠ same type
- MRPS34 p.Arg63His Uncertain significance ★★ ⚠ same type
- MRPS34 p.Arg9Gln Uncertain significance ★★ ⚠ same type
- MRPS34 p.Glu39Asp Uncertain significance ★★ ⚠ same type
- MRPS34 p.Ser84Phe 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/eme2-p-ser317 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown