BMP6 p.Val368=
c.1104G>C · rs17557 · VCV3059297
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 75.7%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
1
BMP6-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 -0.2 | GERP -3.7, phastCons 0.28 |
| Overall | ||
| CADD | 4.822 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
75.7%
East Asian · 33,968/44,860 alleles
Filtering AF
75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 74.8%
Overall
41.6%
671,866/1,613,878 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 75.7% | 1 |
| African / African-American | 70.5% | 1 |
| Admixed American | 64.5% | 2 |
| Amishnot grpmax-eligible | 53.9% | 2 |
| Remaining individualsnot grpmax-eligible | 43.1% | 2 |
| Finnishnot grpmax-eligible | 41.8% | 2 |
| South Asian | 39.2% | 3 |
| European (non-Finnish) | 37.7% | 3 |
| Middle Eastern | 37.2% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 31.1% | 3 |
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
- BMP6
- Protein
- p.Val368=
- Coding
- c.1104G>C
- MANE Select
- NM_001718
- dbSNP
- rs17557
- Type
- single nucleotide variant
- Location
- chr6:7862398 (GRCh38)
- Gene constraint
- LOEUF 0.523 · pLI 0.94 (gnomAD)
- Structure
- AlphaFold pLDDT 69.74 · 5 PDB
- Residue 368
- a UniProt-annotated variant site (in io; associated with disease susceptibility)
Disease context
BMP6-related disorder
Similar variants
- BMP6 c.1392+7T>G Likely benign same condition
- BMP6 c.665-3T>C Likely benign same condition
- BMP6 p.Ala189= Likely benign same condition
- BMP6 p.Ala189Thr Benign same condition
- BMP6 p.Ala212= Benign same condition
- BMP6 p.Ala343= Benign same condition
- BMP6 p.Arg28Gln Benign same condition
- BMP6 p.Arg396= Likely benign 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/bmp6-p-val368 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown