B9D1 p.Pro69=
c.207C>T · rs1598083208 · VCV725568
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.2 | GERP -0.78, phastCons 0.84 |
| Overall | ||
| CADD | 8.669 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- B9D1
- Protein
- p.Pro69=
- Coding
- c.207C>T
- MANE Select
- NM_015681
- dbSNP
- rs1598083208
- Type
- single nucleotide variant
- Location
- chr17:19357877 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.05
- Residue 69
- the c2 b9-type domain
Similar variants
- B9D1 c.341+2T>C Pathogenic/Likely pathogenic ★★ same type
- B9D1 p.Arg114Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- B9D1 p.Arg156Trp Pathogenic/Likely pathogenic ★★ same type
- B9D1 c.404+5G>C Uncertain significance ★★ same type
- B9D1 p.Ala44Val Uncertain significance ★★ ⚠ same type
- B9D1 p.Arg101Gln Uncertain significance ★★ same type
- B9D1 p.Arg140Gln Uncertain significance ★★ ⚠ same type
- B9D1 p.Arg162His Uncertain significance ★★ ⚠ same type
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/b9d1-p-pro69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown