Is BMPER p.Ala9fs (c.26_35delinsAGACCAGAGCGGCG) pathogenic?

BMPER p.Ala9fs (c.2635delinsAGACCAGAGCGGCG) is classified Pathogenic in BMPER (ClinVar, No assertion criteria, 1 submitter; last evaluated 2010-10-08). Absent from gnomAD; Associated with diaphanospondylodysostosis.

What condition is associated with BMPER p.Ala9fs (c.26_35delinsAGACCAGAGCGGCG)?

BMPER p.Ala9fs (c.26_35delinsAGACCAGAGCGGCG) is associated with diaphanospondylodysostosis (ClinVar).

How common is BMPER p.Ala9fs (c.26_35delinsAGACCAGAGCGGCG) in the general population?

BMPER p.Ala9fs (c.26_35delinsAGACCAGAGCGGCG) is absent from gnomAD (gnomAD).

BMPER p.Ala9fs

c.26_35delinsAGACCAGAGCGGCG · rs2128599896 · VCV30743

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

diaphanospondylodysostosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.2	GERP 2.1, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BMPER
Protein: p.Ala9fs
Coding: c.26_35delinsAGACCAGAGCGGCG
MANE Select: NM_001365308
dbSNP: rs2128599896
Type: Indel
Location: chr7:33905639 (GRCh38)
Gene constraint: LOEUF 0.652 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 80.24

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.Ala9Thr Uncertain significance ★ ⚠ same residue
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

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-ala9fs (accessed [today's date]).

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