CCN6 p.Asp28=
c.84T>C · rs782558276 · VCV2874492
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
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 -1.8 | GERP -2.9 |
| Overall | ||
| CADD | 0.628 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,918 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.000434%
7/1,614,032 alleles · very rare
exomes 6/1,461,866 · genomes 1/152,166 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 74,918 |
| South Asian | 0.0011% | 91,080 |
| European (non-Finnish) | 0.000424% | 236,006 |
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.Asp28=
- Coding
- c.84T>C
- MANE Select
- NM_198239
- dbSNP
- rs782558276
- Type
- single nucleotide variant
- Location
- chr6:112061026 (GRCh38)
- Gene constraint
- LOEUF 1.055 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.30
Similar variants
- CCN6 p.Asp28Gly Uncertain significance ★ ⚠ 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
- CCN6 p.Cys78Tyr 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-asp28 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown