SERAC1 p.Ile613=
c.1839T>A · rs745780427 · VCV2163961
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.44 | acceptor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -2.1, phastCons 0.99 |
| Overall | ||
| CADD | 0.896 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Remaining individualsnot grpmax-eligible | 0.0146% | 6,848 |
| European (non-Finnish)grpmax | 0.00401% | 24,967 |
| African / African-American | 0.00136% | 73,646 |
Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- SERAC1
- Protein
- p.Ile613=
- Coding
- c.1839T>A
- MANE Select
- NM_032861
- dbSNP
- rs745780427
- Type
- single nucleotide variant
- Location
- chr6:158111492 (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-ile613 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown