MPC1 p.Thr104=
c.312T>A · rs1583054368 · VCV745683
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 -0.22 | GERP -1.5 |
| Overall | ||
| CADD | 5.366 | 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
- MPC1
- Protein
- p.Thr104=
- Coding
- c.312T>A
- MANE Select
- NM_016098
- dbSNP
- rs1583054368
- Type
- single nucleotide variant
- Location
- chr6:166365447 (GRCh38)
- Gene constraint
- LOEUF 0.919 · pLI 0.10 (gnomAD)
- Structure
- AlphaFold pLDDT 92.85 · 13 PDB
- Residue 104
- an α-helix
Similar variants
- MPC1 p.Arg76Gln Uncertain significance ★★ ⚠ same type
- MPC1 p.Glu102Lys Uncertain significance ★★ ⚠ same type
- MPC1 p.Thr106Met Uncertain significance ★★ ⚠ same type
- MPC1 c.72-8C>T Likely benign ★★ same type
- MPC1 p.Ala10= Benign/Likely benign ★★ same type
- MPC1 p.His101= Benign ★★ same type
- MPC1 p.Leu36Ile Benign ★★ same type
- MPC1 p.Ala70Thr Likely pathogenic ★ 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/mpc1-p-thr104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown