CLN6 p.Pro94=
c.282C>A · rs139261571 · VCV136796
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.19%, amr)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.31 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP -0.69, phastCons 1 |
| Overall | ||
| CADD | 8.743 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.19%
Admixed American · 114/60,026 alleles
Filtering AF
0.162%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.151%
Overall
0.0113%
182/1,613,556 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.19% | 527 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,463 |
| European (non-Finnish) | 0.00441% | 22,682 |
| African / African-American | 0.00266% | 37,529 |
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
- CLN6
- Protein
- p.Pro94=
- Coding
- c.282C>A
- MANE Select
- NM_017882
- dbSNP
- rs139261571
- Type
- single nucleotide variant
- Location
- chr15:68214305 (GRCh38)
- Gene constraint
- LOEUF 1.015 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.86
Similar variants
- CLN6 c.297+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CLN6 c.486+1G>A Likely pathogenic ★★ same condition
- CLN6 c.543-1G>A Likely pathogenic ★★ same condition
- CLN6 c.665+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CLN6 c.84-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CLN6 p.Arg103Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CLN6 p.Arg149Cys Likely pathogenic ★★ same condition
- CLN6 p.Arg28Lys Pathogenic ★★ ⚠ same condition
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/cln6-p-pro94 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown