CLN5 p.Leu309=
c.925T>C · rs1316505069 · VCV1123526
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
neuronal ceroid lipofuscinosis
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 0.33 | GERP -2.1, phastCons 0.8 |
| Overall | ||
| CADD | 3.845 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,860 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000435%
7/1,609,820 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,860 |
| European (non-Finnish) | 0.000509% | 196,414 |
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
- CLN5
- Protein
- p.Leu309=
- Coding
- c.925T>C
- MANE Select
- NM_006493
- dbSNP
- rs1316505069
- Type
- single nucleotide variant
- Location
- chr13:77000817 (GRCh38)
- Gene constraint
- LOEUF 1.197 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.05 · 1 PDB
- Residue 309
- the 'membrane-anchoring' region
Similar variants
- CLN5 p.Leu309fs Pathogenic ★★ same residue
- CLN5 c.174-2A>G Likely pathogenic ★★ same condition
- CLN5 p.Arg150Ter Pathogenic ★★ same condition
- CLN5 p.Arg63His Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CLN5 p.Arg96Ter Pathogenic/Likely pathogenic ★★ same condition
- CLN5 p.Asn143Ser Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CLN5 p.Cys77Tyr Likely pathogenic ★★ ⚠ same condition
- CLN5 p.Gln183Ter Pathogenic/Likely 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/cln5-p-leu309 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown