MARS2 p.Leu403=
c.1207T>C · rs374479698 · VCV758671
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0264%, nfe)
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 0.28 | GERP -1, phastCons 0.36 |
| Overall | ||
| CADD | 7.315 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0264%
European (non-Finnish) · 311/1,180,054 alleles
Filtering AF
0.0239%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0229%
Overall
0.0198%
320/1,614,128 alleles · ultra-rare
exomes 310/1,461,888 · genomes 10/152,240 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0264% | 3,794 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,414 |
| African / African-American | 0.004% | 24,979 |
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
- MARS2
- Protein
- p.Leu403=
- Coding
- c.1207T>C
- MANE Select
- NM_138395
- dbSNP
- rs374479698
- Type
- single nucleotide variant
- Location
- chr2:197706612 (GRCh38)
- Gene constraint
- LOEUF 0.952 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.66
Similar variants
- MARS2 p.Ala141Val Uncertain significance ★★ ⚠ same type
- MARS2 p.Ala402Ser Uncertain significance ★★ ⚠ same type
- MARS2 p.Arg142Trp Uncertain significance ★★ ⚠ same type
- MARS2 p.Arg224Gln Uncertain significance ★★ ⚠ same type
- MARS2 p.Arg409Gly Uncertain significance ★★ ⚠ same type
- MARS2 p.Arg414Ile Uncertain significance ★★ ⚠ same type
- MARS2 p.Arg568Gly Uncertain significance ★★ ⚠ same type
- MARS2 p.Arg592Gln 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/mars2-p-leu403 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown