SUCLA2 p.Arg164=
c.490A>C · rs745493625 · VCV387994
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 2.1 | GERP -0.17, phastCons 1 |
| Overall | ||
| CADD | 6.358 | 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
- SUCLA2
- Protein
- p.Arg164=
- Coding
- c.490A>C
- MANE Select
- NM_003850
- dbSNP
- rs745493625
- Type
- single nucleotide variant
- Location
- chr13:47988585 (GRCh38)
- Gene constraint
- LOEUF 0.713 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.45 · 2 PDB
- Residue 164
- the atp-grasp domain; a β-strand
Similar variants
- SUCLA2 p.Arg164Gly Uncertain significance ★ ⚠ same residue
- SUCLA2 c.534+1G>A Pathogenic ★★ same type
- SUCLA2 p.Ala307Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- SUCLA2 p.Arg160Ter Pathogenic/Likely pathogenic ★★ same type
- SUCLA2 p.Arg284Cys Pathogenic/Likely pathogenic ★★ same type
- SUCLA2 p.Asp333Gly Pathogenic/Likely pathogenic ★★ same type
- SUCLA2 c.1228+4A>G Uncertain significance ★★ same type
- SUCLA2 p.Ala12Val 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/sucla2-p-arg164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown