MC3R p.Pro15=
c.45T>A · VCV3355557
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000508%, 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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.3 | GERP -2.8 |
| Overall | ||
| CADD | 0.141 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000508%
European (non-Finnish) · 6/1,180,036 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000372%
6/1,614,058 alleles · very rare
exomes 4/1,461,868 · genomes 2/152,190 · 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.Pro15=
- Coding
- c.45T>A
- MANE Select
- NM_019888
- Type
- single nucleotide variant
- Location
- chr20:56248888 (GRCh38)
- Gene constraint
- LOEUF 1.196 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.32 · 6 PDB
Disease context
MC3R-related disorder
Similar variants
- 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
- MC3R p.Cys315Arg 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-pro15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown