SERAC1 p.Val280=
c.840A>T · rs2128415848 · VCV1605036
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome
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 -0.49 | GERP -3.7, phastCons 0.12 |
| Overall | ||
| CADD | 5.154 | 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
- SERAC1
- Protein
- p.Val280=
- Coding
- c.840A>T
- MANE Select
- NM_032861
- dbSNP
- rs2128415848
- Type
- single nucleotide variant
- Location
- chr6:158130385 (GRCh38)
- Gene constraint
- LOEUF 0.681 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.66
Disease context
3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor MEGDEL syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- SERAC1 c.1403+1G>C Pathogenic ★★ same condition
- SERAC1 p.Arg148Ter Pathogenic ★★ same condition
- SERAC1 p.Arg368Ter Pathogenic ★★ same condition
- SERAC1 p.Arg387Ter Pathogenic/Likely pathogenic ★★ same condition
- SERAC1 p.Arg447Ter Pathogenic ★★ same condition
- SERAC1 p.Arg68Ter Pathogenic/Likely pathogenic ★★ same condition
- SERAC1 p.Gln376Ter Pathogenic ★★ same condition
- SERAC1 p.Ser498Thr Pathogenic/Likely pathogenic ★★ same condition
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/serac1-p-val280 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown