Is BMPER p.Gly362= (c.1086C>T) pathogenic?

BMPER p.Gly362= (c.1086C>T) is classified Benign in BMPER (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-02-03). Low-frequency (popmax 2.52%, afr); Associated with diaphanospondylodysostosis.

What condition is associated with BMPER p.Gly362= (c.1086C>T)?

BMPER p.Gly362= (c.1086C>T) is associated with diaphanospondylodysostosis (ClinVar).

How common is BMPER p.Gly362= (c.1086C>T) in the general population?

BMPER p.Gly362= (c.1086C>T) is low-frequency (popmax 2.52%, afr) (gnomAD).

BMPER p.Gly362=

c.1086C>T · rs116085783 · VCV360107

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.52%, afr)

Conditions

diaphanospondylodysostosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.26 · evaluated, not missing
Constraint at this position
Conservation	phyloP -1.1	GERP -0.41, phastCons 0.001
Overall
CADD	7.668	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.52% African / African-American · 1,893/75,002 alleles

Filtering AF 2.43% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.39%

Overall 0.141% 2,268/1,614,084 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.52%	40
Admixed American	0.253%	395
Remaining individualsnot grpmax-eligible	0.21%	477
Middle Eastern	0.0495%	2,021
South Asian	0.00769%	13,010
European (non-Finnish)	0.00686%	14,568
Finnishnot grpmax-eligible	0.00156%	64,034

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: BMPER
Protein: p.Gly362=
Coding: c.1086C>T
MANE Select: NM_001365308
dbSNP: rs116085783
Type: single nucleotide variant
Location: chr7:34078864 (GRCh38)
Gene constraint: LOEUF 0.652 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 80.24
Residue 362: the vwfd domain

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

Disease context

diaphanospondylodysostosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BMPER p.Arg241Ter Likely pathogenic ★★ same condition
BMPER p.Gln309Ter Pathogenic ★★ same condition
BMPER p.Ala39Ser Uncertain significance ★★ ⚠ same condition
BMPER p.Ala486Val Uncertain significance ★★ ⚠ same condition
BMPER p.Arg131Cys Uncertain significance ★★ ⚠ same condition
BMPER p.Arg505His Uncertain significance ★★ ⚠ same condition
BMPER p.Arg582Gln Uncertain significance ★★ ⚠ same condition
BMPER p.Arg582Trp 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/bmper-p-gly362 (accessed [today's date]).

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