Is CLN6 p.Arg5= (c.15G>A) pathogenic?

CLN6 p.Arg5= (c.15G>A) is classified Likely benign in CLN6 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-31). Very rare (popmax 0.00135%, nfe); Associated with neuronal ceroid lipofuscinosis.

What condition is associated with CLN6 p.Arg5= (c.15G>A)?

CLN6 p.Arg5= (c.15G>A) is associated with neuronal ceroid lipofuscinosis (ClinVar).

How common is CLN6 p.Arg5= (c.15G>A) in the general population?

CLN6 p.Arg5= (c.15G>A) is very rare (popmax 0.00135%, nfe) (gnomAD).

CLN6 p.Arg5=

c.15G>A · rs1008565735 · VCV1149688

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00135%, 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 -0.14	GERP -1.3, phastCons 0.53
Overall
CADD	11.82	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00135% European (non-Finnish) · 15/1,114,330 alleles

Filtering AF 0.000808% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000641%

Overall 0.00109% 16/1,467,454 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00135%	74,289
South Asian	0.00128%	78,140

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.Arg5=
Coding: c.15G>A
MANE Select: NM_017882
dbSNP: rs1008565735
Type: single nucleotide variant
Location: chr15:68229570 (GRCh38)
Gene constraint: LOEUF 1.015 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.86

Full CLN6 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

CLN6 p.Arg5Gln Uncertain significance ★ ⚠ same residue
CLN6 p.Arg5Trp Conflicting classifications of pathogenicity ★ ⚠ same residue
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

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-arg5 (accessed [today's date]).

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