CNTN6 p.Val8=
c.24A>G · VCV4960961
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0243%, 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 2.1 | GERP 0.71, phastCons 1 |
| Overall | ||
| CADD | 8.182 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0243%
South Asian · 22/90,684 alleles
Filtering AF
0.0163%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0138%
Overall
0.00454%
73/1,608,262 alleles · ultra-rare
exomes 71/1,456,140 · genomes 2/152,122 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0243% | 4,122 |
| European (non-Finnish) | 0.00408% | 24,496 |
| Remaining individualsnot grpmax-eligible | 0.00322% | 31,069 |
| African / African-American | 0.00134% | 74,834 |
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
- CNTN6
- Protein
- p.Val8=
- Coding
- c.24A>G
- MANE Select
- NM_001289080
- Type
- single nucleotide variant
- Location
- chr3:1148032 (GRCh38)
- Gene constraint
- LOEUF 1.316 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 86.19
Similar variants
- CNTN6 c.1213+8G>A Benign ★★ same type
- CNTN6 p.Ala440Ser Benign ★★ same type
- CNTN6 p.Arg135Ter Benign ★★ same type
- CNTN6 p.Arg303Gln Likely benign ★★ same type
- CNTN6 p.Gly1001= Benign/Likely benign ★★ same type
- CNTN6 p.Gly96= Benign ★★ same type
- CNTN6 p.Ile1024Leu Benign ★★ same type
- CNTN6 p.Ile529Leu Benign/Likely benign ★★ 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/cntn6-p-val8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown