PDHX p.Phe445=
c.1335C>T · rs2494783806 · VCV2847963
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. | ||
| REVEL | 0.017 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.86 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 8.886 | 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
- PDHX
- Protein
- p.Phe445=
- Coding
- c.1335C>T
- MANE Select
- NM_003477
- dbSNP
- rs2494783806
- Type
- single nucleotide variant
- Location
- chr11:34995001 (GRCh38)
- Gene constraint
- LOEUF 0.797 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.13 · 5 PDB
Similar variants
- PDHX p.Phe445Val Benign/Likely benign ★★ same residue
- PDHX p.Arg284Ter Pathogenic ★★ same type
- PDHX p.Arg446Ter Pathogenic/Likely pathogenic ★★ same type
- PDHX p.Arg476Ter Likely pathogenic ★★ same type
- PDHX p.Gln248Ter Pathogenic ★★ same type
- PDHX p.Gln411Ter Pathogenic/Likely pathogenic ★★ same type
- PDX1 p.Lys191Gln Likely pathogenic ★★ same type
- PDHX c.1023+2267A>G 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/pdhx-p-phe445 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown