Is CLN5 p.Val5= (c.15A>G) pathogenic?

CLN5 p.Val5= (c.15A>G) is classified Likely benign in CLN5 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-04). Very rare (popmax 8.48e-05%, nfe); Associated with neuronal ceroid lipofuscinosis.

What condition is associated with CLN5 p.Val5= (c.15A>G)?

CLN5 p.Val5= (c.15A>G) is associated with neuronal ceroid lipofuscinosis (ClinVar).

How common is CLN5 p.Val5= (c.15A>G) in the general population?

CLN5 p.Val5= (c.15A>G) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

CLN5 p.Val5=

c.15A>G · rs2034185809 · VCV1123933

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Conditions

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 -0.08	GERP -2
Overall
CADD	6.257	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,300 alleles

Overall 6.85e-05% 1/1,459,534 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.Val5=
Coding: c.15A>G
MANE Select: NM_006493
dbSNP: rs2034185809
Type: single nucleotide variant
Location: chr13:76992113 (GRCh38)
Gene constraint: LOEUF 1.197 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.05 · 1 PDB

Full CLN5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

neuronal ceroid lipofuscinosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CLN5 p.Val5Ile Uncertain significance ★★ ⚠ same residue
CLN5 p.Leu5Pro Uncertain significance ★ 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

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-val5 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown