Is BMPR2 p.His800= (c.2400T>C) pathogenic?

BMPR2 p.His800= (c.2400T>C) is classified Likely benign in BMPR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-02). Very rare (popmax 0.00266%, afr); Associated with Inborn genetic diseases.

What condition is associated with BMPR2 p.His800= (c.2400T>C)?

BMPR2 p.His800= (c.2400T>C) is associated with Inborn genetic diseases (ClinVar).

How common is BMPR2 p.His800= (c.2400T>C) in the general population?

BMPR2 p.His800= (c.2400T>C) is very rare (popmax 0.00266%, afr) (gnomAD).

BMPR2 p.His800=

c.2400T>C · VCV4214478

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00266%, afr)

Conditions

Inborn genetic diseases

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 -1.1	GERP -4, phastCons 0.003
Overall
CADD	4.306	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00266% African / African-American · 2/75,050 alleles

Filtering AF 0.000442% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000166%

Overall 0.000124% 2/1,614,202 alleles · very rare exomes 2/1,461,894 · genomes 0/152,308 · 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: BMPR2
Protein: p.His800=
Coding: c.2400T>C
MANE Select: NM_001204
Type: single nucleotide variant
Location: chr2:202556065 (GRCh38)
Gene constraint: LOEUF 0.376 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 58.07 · 7 PDB
Residue 800: a UniProt-annotated variant site (in pph1; changed localization to the plasma membrane); a UniProt-annotated variant site (in pph1; loss of localization to the plasma membrane; localized to the cytoplasm)

Full BMPR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BMPR2 p.His800Arg Uncertain significance ★ ⚠ same residue
BMPR2 p.His800Asn Uncertain significance ★ ⚠ same residue
BMPR2 p.His800Gln Uncertain significance ★ ⚠ same residue
BMPR2 p.His800Tyr Uncertain significance ★ ⚠ same residue
BMPR2 p.Ala35Val Uncertain significance ★★ ⚠ same condition
BMPR2 p.Arg114His Uncertain significance ★★ ⚠ same condition
BMPR2 p.Arg357Lys Uncertain significance ★★ ⚠ same condition
BMPR2 p.Arg857Trp 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/bmpr2-p-his800 (accessed [today's date]).

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