CNTLN p.Pro509Ser
c.1525C>T · VCV4655066
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.5e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.131 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.60 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 2.6, phastCons 1 |
| Regional constraint | o/e 1.30 | unconstrained · MANE · 368 kb · p 1.7e-33 · regional, not allelic |
| Overall | ||
| CADD | 24.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.5e-05%
European (non-Finnish) · 1/1,176,196 alleles
Overall
6.23e-05%
1/1,604,990 alleles · very rare
exomes 0/1,453,034 · genomes 1/151,956 · 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
- CNTLN
- Protein
- p.Pro509Ser
- Coding
- c.1525C>T
- MANE Select
- NM_017738
- Type
- single nucleotide variant
- Location
- chr9:17332611 (GRCh38)
- Gene constraint
- LOEUF 1.431 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.14
- Residue 509
- the 'disordered' region
Similar variants
- CNTLN p.Phe935Leu Uncertain significance ★★ same type
- CNTLN c.3115-9A>T Benign ★★ same type
- CNTLN p.Ala1256= Benign ★★ same type
- CNTLN p.Asp553Glu Benign ★★ same type
- CNTLN p.Gln800= Benign ★★ same type
- CNTLN p.Ser404Asn Benign ★★ same type
- CNTLN p.Ala1005Val Uncertain significance ★ same type
- CNTLN p.Ala1248Thr 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/cntln-p-pro509ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown