BMPER p.Thr606=
c.1818C>A · rs138797097 · VCV360116
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.241%, nfe)
Conditions
1
diaphanospondylodysostosis
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 -0.49 | GERP -3, phastCons 0.027 |
| Overall | ||
| CADD | 4.046 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.241%
European (non-Finnish) · 2,849/1,179,936 alleles
Filtering AF
0.234%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.231%
Overall
0.182%
2,938/1,613,896 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.241% | 414 |
| Remaining individualsnot grpmax-eligible | 0.0864% | 1,157 |
| Middle Eastern | 0.033% | 3,031 |
| African / African-American | 0.0307% | 3,260 |
| Admixed American | 0.00834% | 11,994 |
| Finnishnot grpmax-eligible | 0.00781% | 12,802 |
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.Thr606=
- Coding
- c.1818C>A
- MANE Select
- NM_001365308
- dbSNP
- rs138797097
- Type
- single nucleotide variant
- Location
- chr7:34143302 (GRCh38)
- Gene constraint
- LOEUF 0.652 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.24
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-thr606 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown