MTRR p.Pro172=
c.516T>C · rs1579656831 · VCV1089310
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
methylcobalamin deficiency type cblE
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.048 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -5.1 | GERP -3.5 |
| Overall | ||
| CADD | 0.447 | 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
- MTRR
- Protein
- p.Pro172=
- Coding
- c.516T>C
- MANE Select
- NM_002454
- dbSNP
- rs1579656831
- Type
- single nucleotide variant
- Location
- chr5:7878058 (GRCh38)
- Gene constraint
- LOEUF 0.932 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 85.79 · 2 PDB
- Residue 172
- the 'hinge' region
Disease context
methylcobalamin deficiency type cblE — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Homocystinuria without methylmalonic aciduria (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- All ages
Similar variants
- MTRR c.1057+1G>A Likely pathogenic ★★ same condition
- MTRR c.1146+1G>A Likely pathogenic ★★ same condition
- MTRR c.1371-1G>A Likely pathogenic ★★ same condition
- MTRR c.1676+2T>C Likely pathogenic ★★ same condition
- MTRR c.1677-1G>A Pathogenic/Likely pathogenic ★★ same condition
- MTRR c.1769+1G>A Pathogenic/Likely pathogenic ★★ same condition
- MTRR c.401+1G>A Likely pathogenic ★★ same condition
- MTRR c.402-1G>T Likely pathogenic ★★ same condition
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/mtrr-p-pro172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown