CLN5 p.Arg43=
c.129G>C · rs746845935 · VCV2046335
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.92e-05%)
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 0.18 | GERP 0.087, phastCons 0.001 |
| Overall | ||
| CADD | 5.636 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.92e-05%
Overall
6.92e-05%
1/1,444,434 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
- CLN5
- Protein
- p.Arg43=
- Coding
- c.129G>C
- MANE Select
- NM_006493
- dbSNP
- rs746845935
- Type
- single nucleotide variant
- Location
- chr13:76992227 (GRCh38)
- Gene constraint
- LOEUF 1.197 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.05 · 1 PDB
- Residue 43
- a functional site (cleavage; by sppl3)
Similar variants
- 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
- CLN5 p.Gln194Ter 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-arg43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown