DLAT p.Cys164=
c.492T>C · rs782662937 · VCV734764
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, 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 2.9 | GERP -0.19, phastCons 1 |
| Overall | ||
| CADD | 11.81 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,908 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.000867%
14/1,614,058 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,727 |
| Admixed American | 0.00167% | 59,998 |
| European (non-Finnish) | 0.000763% | 131,117 |
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
- DLAT
- Protein
- p.Cys164=
- Coding
- c.492T>C
- MANE Select
- NM_001931
- dbSNP
- rs782662937
- Type
- single nucleotide variant
- Location
- chr11:112028625 (GRCh38)
- Gene constraint
- LOEUF 0.759 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.59 · 13 PDB
- Residue 164
- the lipoyl-binding 1 domain; a β-strand
Similar variants
- DLAT p.Cys164Ser Uncertain significance ★ ⚠ same residue
- DLAT c.976-1G>A Pathogenic/Likely pathogenic ★★ same type
- DLAT p.Arg435Ter Pathogenic ★★ same type
- DLAT p.Glu138Ter Pathogenic ★★ same type
- DLAT p.Val157Gly Likely pathogenic ★★ same type
- DLAT c.1130-6T>G Uncertain significance ★★ same type
- DLAT p.Ala109Thr Uncertain significance ★★ ⚠ same type
- DLAT p.Ala191Gly 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/dlat-p-cys164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown