EPRS1 p.Ser747=
c.2241T>C · rs905979046 · VCV2021141
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -0.021 | GERP -2.8, phastCons 0.005 |
| Overall | ||
| CADD | 6.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- EPRS1
- Protein
- p.Ser747=
- Coding
- c.2241T>C
- MANE Select
- NM_004446
- dbSNP
- rs905979046
- Type
- single nucleotide variant
- Location
- chr1:219997283 (GRCh38)
- Gene constraint
- LOEUF 0.549 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 83.55 · 33 PDB
- Residue 747
- the 'glutamate--trna ligase' region; a modified residue (phosphoserine); a UniProt-annotated variant site (in hld15)
Similar variants
- EPRS1 p.Ser747Tyr Likely benign ★ ⚠ same residue
- EPRS1 p.Arg1278Ter Pathogenic/Likely pathogenic ★★ same type
- EPRS1 p.Gln985Ter Pathogenic ★★ same type
- EPRS1 c.4244+3A>C Uncertain significance ★★ same type
- EPRS1 p.Ala1183Val Uncertain significance ★★ ⚠ same type
- EPRS1 p.Ala174Thr Uncertain significance ★★ ⚠ same type
- EPRS1 p.Ala301Thr Uncertain significance ★★ ⚠ same type
- EPRS1 p.Ala901Val 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/eprs1-p-ser747 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown