CNTLN p.Asp863=
c.2589C>T · VCV4655080
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0253%, sas)
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 -0.17 | GERP -1.6, phastCons 0.26 |
| Overall | ||
| CADD | 9.231 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0253%
South Asian · 23/90,772 alleles
Filtering AF
0.0172%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0146%
Overall
0.00683%
110/1,610,090 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0253% | 3,947 |
| African / African-American | 0.0107% | 9,369 |
| European (non-Finnish) | 0.00646% | 15,488 |
| Admixed American | 0.00334% | 29,942 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,358 |
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.Asp863=
- Coding
- c.2589C>T
- MANE Select
- NM_017738
- Type
- single nucleotide variant
- Location
- chr9:17395043 (GRCh38)
- Gene constraint
- LOEUF 1.431 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.14
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-asp863 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown