MCHR2 p.Asp179=
c.537C>T · rs139619654 · VCV786094
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.742%, afr)
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 -1.2 | GERP -2.7 |
| Overall | ||
| CADD | 7.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.742%
African / African-American · 556/74,966 alleles
Filtering AF
0.691%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.67%
Overall
0.0435%
702/1,612,820 alleles · rare
exomes 388/1,460,650 · genomes 314/152,170 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.742% | 135 |
| Middle Eastern | 0.0827% | 1,210 |
| Admixed American | 0.0651% | 1,536 |
| Remaining individualsnot grpmax-eligible | 0.0593% | 1,688 |
| European (non-Finnish) | 0.00526% | 19,019 |
| South Asian | 0.0033% | 30,326 |
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
- MCHR2
- Protein
- p.Asp179=
- Coding
- c.537C>T
- MANE Select
- NM_001040179
- dbSNP
- rs139619654
- Type
- single nucleotide variant
- Location
- chr6:99942999 (GRCh38)
- Gene constraint
- LOEUF 0.973 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.66 · 1 PDB
- Residue 179
- an α-helix
Similar variants
- MCHR2 p.Ala160Val Uncertain significance ★ ⚠ same type
- MCHR2 p.Ala165Ser Uncertain significance ★ ⚠ same type
- MCHR2 p.Ala234Asp Uncertain significance ★ ⚠ same type
- MCHR2 p.Ala283Asp Uncertain significance ★ ⚠ same type
- MCHR2 p.Arg140Gln Uncertain significance ★ ⚠ same type
- MCHR2 p.Arg140Leu Uncertain significance ★ ⚠ same type
- MCHR2 p.Arg143Cys Uncertain significance ★ ⚠ same type
- MCHR2 p.Arg145Lys 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/mchr2-p-asp179 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown