CLN6 p.Pro79=
c.237C>A · VCV3687188
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000509%, nfe)
Conditions
1
neuronal ceroid lipofuscinosis
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.315 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.47 | GERP 1.6, phastCons 0.98 |
| Overall | ||
| CADD | 7.624 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000509%
European (non-Finnish) · 6/1,179,936 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000372%
6/1,613,974 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
- CLN6
- Protein
- p.Pro79=
- Coding
- c.237C>A
- MANE Select
- NM_017882
- Type
- single nucleotide variant
- Location
- chr15:68214350 (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-pro79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown