CCN6 p.Gln289=
c.867G>A · rs782019386 · VCV2751379
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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.98 | GERP 1.6, phastCons 0.99 |
| Overall | ||
| CADD | 3.451 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,856 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,613,520 alleles · very rare
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
- CCN6
- Protein
- p.Gln289=
- Coding
- c.867G>A
- MANE Select
- NM_198239
- dbSNP
- rs782019386
- Type
- single nucleotide variant
- Location
- chr6:112069422 (GRCh38)
- Gene constraint
- LOEUF 1.055 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.30
- Residue 289
- a disulfide bond; a UniProt-annotated variant site (in pprd); the ctck domain
Similar variants
- CCN6 p.Gln289His Uncertain significance ★★ ⚠ same residue
- CCN6 p.Gln289fs Pathogenic/Likely pathogenic ★★ same residue
- CCN6 c.49-1G>A Pathogenic/Likely pathogenic ★★ same type
- CCN6 c.590-1G>C Likely pathogenic ★★ same type
- CCN6 p.Ala197Pro Pathogenic/Likely pathogenic ★★ ⚠ same type
- CCN6 p.Cys223Gly Pathogenic ★★ same type
- CCN6 p.Cys337Tyr Pathogenic/Likely pathogenic ★★ same type
- CCN6 p.Cys52Ter Pathogenic/Likely pathogenic ★★ 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/ccn6-p-gln289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown