SEPTIN9 p.Pro145=
c.435G>C · rs766609199 · VCV1682603
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.3 | GERP -4.8 |
| Overall | ||
| CADD | 0.202 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,040 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,610,862 alleles · very rare
exomes 2/1,458,568 · genomes 0/152,294 · 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
- SEPTIN9
- Protein
- p.Pro145=
- Coding
- c.435G>C
- MANE Select
- NM_001113491
- dbSNP
- rs766609199
- Type
- single nucleotide variant
- Location
- chr17:77402417 (GRCh38)
- Gene constraint
- LOEUF 0.39 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 67.42 · 3 PDB
- Residue 145
- the 'disordered' region; a UniProt-annotated variant site (in)
Similar variants
- SEPTIN9 p.Pro145Leu Benign/Likely benign ★★ same residue
- SEPTIN9 p.Arg106Trp Pathogenic ★★ same type
- SEPTIN9 c.1380+5G>C Uncertain significance ★★ same type
- SEPTIN9 p.Ala183Val Uncertain significance ★★ ⚠ same type
- SEPTIN9 p.Ala201Thr Uncertain significance ★★ ⚠ same type
- SEPTIN9 p.Ala234Val Uncertain significance ★★ ⚠ same type
- SEPTIN9 p.Ala266Thr Uncertain significance ★★ ⚠ same type
- SEPTIN9 p.Ala571Thr 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/septin9-p-pro145 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown