PDHA1 p.Lys149=
c.447A>G · rs773139249 · VCV2575762
Likely pathogenic
Single submitter
Classification
Likely pathogenic
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/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.49 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.25 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 3.1 | GERP 0.84, phastCons 1 |
| Overall | ||
| CADD | 3.482 | 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
- PDHA1
- Protein
- p.Lys149=
- Coding
- c.447A>G
- MANE Select
- NM_000284
- dbSNP
- rs773139249
- Type
- single nucleotide variant
- Location
- chrX:19353110 (GRCh38)
- Structure
- AlphaFold pLDDT 94.77 · 9 PDB
Similar variants
- PDHA1 p.Ala169Val Pathogenic ★★★ same type
- PDHA1 p.Arg304Ter Pathogenic ★★★ same type
- PDHA1 p.Arg378Cys Pathogenic ★★★ ⚠ same type
- PDHA1 p.Arg72Cys Likely pathogenic ★★★ same type
- PDHA1 p.Ile280Ser Uncertain significance ★★★ ⚠ same type
- PDHA1 p.Ala265= Benign ★★★ same type
- PDHA1 p.Glu333Asp Benign ★★★ same type
- PDHA1 p.Met282Leu Benign ★★★ 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/pdha1-p-lys149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown