CLN3 p.Ala196fs
c.586dup · rs386833735 · VCV56286
Likely pathogenic
No assertion criteria
Classification
Likely pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
ultra-rare (gnomAD MAF 1.681e-06)
Conditions
1
neuronal ceroid lipofuscinosis 3
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 9 of 16 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.7, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
dbSNP / gnomAD
Global frequency
0.000168%
via dbSNP · ultra-rare
No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.
Variant & gene context
- Gene
- CLN3
- Protein
- p.Ala196fs
- Coding
- c.586dup
- MANE Select
- NM_001042432
- dbSNP
- rs386833735
- Type
- Duplication
- Location
- chr16:28486437 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 81.81
Disease context
neuronal ceroid lipofuscinosis 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor CLN3 disease (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy
Similar variants
- CLN3 p.Ala191fs Pathogenic ★★ same condition
- CLN3 p.Arg127fs Pathogenic/Likely pathogenic ★★ same condition
- CLN3 p.Ser208fs Pathogenic ★★ same condition
- CLN3 p.Val374fs Pathogenic/Likely pathogenic ★★ same condition
- CLN3 c.461dup Likely pathogenic ★ same condition
- CLN3 p.Cys353fs Likely pathogenic ★ same condition
- CLN3 p.Leu122fs Likely pathogenic ★ same condition
- CLN3 p.Ser336fs 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/cln3-p-ala196fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown