Is BMP6 p.His369= (c.1107C>T) pathogenic?

BMP6 p.His369= (c.1107C>T) is classified Likely benign in BMP6 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-20). Very rare (popmax 0.00801%, afr); Associated with BMP6-related disorder.

What condition is associated with BMP6 p.His369= (c.1107C>T)?

BMP6 p.His369= (c.1107C>T) is associated with BMP6-related disorder (ClinVar).

How common is BMP6 p.His369= (c.1107C>T) in the general population?

BMP6 p.His369= (c.1107C>T) is very rare (popmax 0.00801%, afr) (gnomAD).

BMP6 p.His369=

c.1107C>T · rs755810484 · VCV3039734

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00801%, afr)

Conditions

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 -3.5	GERP -1.9
Overall
CADD	8.436	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00801% African / African-American · 6/74,938 alleles

Filtering AF 0.00347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00228%

Overall 0.00124% 20/1,614,086 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00801%	12,490
South Asian	0.00549%	18,218
East Asian	0.00445%	22,447
Remaining individualsnot grpmax-eligible	0.0016%	62,490
European (non-Finnish)	0.000508%	196,674

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.His369=
Coding: c.1107C>T
MANE Select: NM_001718
dbSNP: rs755810484
Type: single nucleotide variant
Location: chr6:7862401 (GRCh38)
Gene constraint: LOEUF 0.523 · pLI 0.94 (gnomAD)
Structure: AlphaFold pLDDT 69.74 · 5 PDB
Residue 369: a UniProt-annotated variant site (in io; associated with disease susceptibility)

Full BMP6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-his369 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown