MC3R p.Pro257=
c.771C>G · VCV3355214
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Conditions
1
MC3R-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.27 | GERP -3.8, phastCons 0.19 |
| Overall | ||
| CADD | 8.313 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,080 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,612,976 alleles · very rare
exomes 0/1,460,796 · genomes 2/152,180 · joint denominator
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
- MC3R
- Protein
- p.Pro257=
- Coding
- c.771C>G
- MANE Select
- NM_019888
- Type
- single nucleotide variant
- Location
- chr20:56249614 (GRCh38)
- Gene constraint
- LOEUF 1.196 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.32 · 6 PDB
- Residue 257
- an α-helix
Disease context
MC3R-related disorder
Similar variants
- MC3R p.Pro257His Uncertain significance ★ ⚠ same residue
- MC3R p.Asn91Ser Uncertain significance ★ ⚠ same condition
- MC3R p.Ile57Thr Uncertain significance ★ ⚠ same condition
- MC3R p.Ala223Val Uncertain significance ⚠ same condition
- MC3R p.Ala3Val Uncertain significance ⚠ same condition
- MC3R p.Asn28Lys Uncertain significance ⚠ same condition
- MC3R p.Asn318Lys Uncertain significance ⚠ same condition
- MC3R p.Asn68Lys Uncertain significance ⚠ 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/mc3r-p-pro257 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown