AtlasGene
CLN6
CLN6 transmembrane ER protein
- HGNC 2077↗(opens in a new tab)
- Ensembl gene ENSG00000128973↗(opens in a new tab)
- NCBI Gene 54982↗(opens in a new tab)
Summary
- Cytogenetic location
- 15q23
- Coordinates
- Chromosome 15: 68,206,992–68,229,728 (GRCh38)
- Exons
- 7 exons across 22.7 kb
- Protein
- 311 amino acids
- Also known as
- FLJ20561, HsT18960, nclf
- MANE Select transcript
- ENST00000249806.11NM_017882.3
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
AtlasThis page as data
Add .json to the page's address, or ask for application/json, to read it as JSON.
library(jsonlite)
url <- "https://dantelabs.com/genes/cln6.json"
page <- fromJSON(url)
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Get my Genome TestCurated reports relevant to this gene
Neuronal Ceroid Lipofuscinosis
- Late Infantile Neuronal Ceroid LipofuscinosisAutosomal recessive
A genetically heterogeneous group of neuronal ceroid lipofuscinoses (NCLs) typically characterized by onset during infancy or early childhood with decline of mental and motor capacities, epilepsy, and vision loss through retinal degeneration.
- 5 GenCC submitters rate it definitive or strong
- Autosomal recessive
A group of inherited progressive degenerative brain diseases characterized clinically by a decline of mental and other capacities, epilepsy, and vision loss through retinal degeneration, and histopathologically by intracellular accumulation of an autofluorescent material, ceroid lipofuscin, in the neuronal cells in the brain and in the retina.
- ClinGen rates the link definitive
- 7 GenCC submitters rate it definitive or strong
Broader groupings
Lysosomal Storage Disease
- Lysosomal storage disease (other and unspecified types)
One of 59 genes linked to it
Covers lysosomal storage diseases without a dedicated report, such as Farber disease and other ASAH1-related disorders, prosaposin (PSAP) deficiencies, multiple sulfatase deficiency, mucopolysaccharidosis types IX and X, and Dorfman-Chanarin disease; inheritance varies by subtype, most often autosomal recessive.
- ClinGen rates the link definitive
- 7 GenCC submitters rate it definitive or strong
How CLN6 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 2.2 kb of the gene's 22.7 kb; 936 of those bases code for the protein.
Sequencing CLN6
3Easy
How hard CLN6 is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of CLN6's exons sit where short reads map cleanly.
What adds to it: the share of CLN6's exons in each kind of hard region
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. Weight 35%.0%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 30%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 15%.8.5%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.22%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 10%.0%
A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scoredEach bar is the share of CLN6's exon bases in that kind of difficult region. The score weighs them by how much each costs a short-read call: 0 when no base is in any, 100 when every base is in all of them.
113
positions in CLN6 where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 22.7 kb of CLN6, introns included, not only the 2.2 kb of exons.
ClinVar pathogenic variants (128)
The CLN6 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.
- Pathogenic 65
- Pathogenic/likely pathogenic 7
- Likely pathogenic 56
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_017882.3(CLN6):c.896C>T (p.Pro299Leu) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.791CCT[1] (p.Ser265del) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.768C>G (p.Asp256Glu) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.712_713delinsAC (p.Phe238Thr) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.2(CLN6):c.461_463del (p.Ile154del) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.456del (p.Ile153fs) (opens in a new tab) | neuronal ceroid lipofuscinosis | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.407G>A (p.Arg136His) (opens in a new tab) | neuronal ceroid lipofuscinosis | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.406C>T (p.Arg136Cys) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.395_396del (p.Ser132fs) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.396dup (p.Val133fs) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.316dup (p.Arg106fs) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.308G>A (p.Arg103Gln) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.214G>T (p.Glu72Ter) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.180dup (p.Gly61fs) (opens in a new tab) | neuronal ceroid lipofuscinosis | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.890del (p.Pro297fs) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 1 other | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.775G>A (p.Gly259Ser) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.516T>A (p.Tyr172Ter) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 1 other | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.195dup (p.Met66fs) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 1 other | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.150C>G (p.Tyr50Ter) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 1 other | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.84-1G>A (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.3G>A (p.Met1Ile) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.721A>G (p.Met241Val) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.665+1G>A (opens in a new tab) | neuronal ceroid lipofuscinosis | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.662A>G (p.Tyr221Cys) (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6B (Kufs type) and 1 other | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_017882.3(CLN6):c.486+1G>A (opens in a new tab) | ceroid lipofuscinosis, neuronal, 6A and 2 others | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
See all 128 with every other CLN6 variant in ClinVar → (opens in a new tab)
Genes linked to the same conditions
- CLN5CLN5 lysosomal BMP synthaseShares 3 conditions
- MFSD8major facilitator superfamily domain containing 8Shares 3 conditions
- CLCN6Cl-/H+ antiporter 6Shares 2 conditions
- CLN3CLN3 lysosomal/endosomal transmembrane protein, batteninShares 2 conditions
- CLN8CLN8 transmembrane ER and ERGIC proteinShares 2 conditions
- CTSDcathepsin DShares 2 conditions
- CTSFcathepsin FShares 2 conditions
- DNAJC5DnaJ heat shock protein family (Hsp40) member C5Shares 2 conditions
- GRNgranulin precursorShares 2 conditions
- KCTD7potassium channel tetramerization domain containing 7Shares 2 conditions
- PPT1palmitoyl-protein thioesterase 1Shares 2 conditions
- TPP1tripeptidyl peptidase 1Shares 2 conditions
Traits linked to CLN6
The Human Phenotype Ontology lists these as features of the rare conditions CLN6 can cause. Each trait's page lists the other genes linked to it.
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-18: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.18-8b139e39.
Cite this page
Dante Labs. (n.d.). CLN6 gene: CLN6 transmembrane ER protein. Retrieved 18 October 2026, from https://dantelabs.com/genes/cln6
Dante Labs. CLN6 gene: CLN6 transmembrane ER protein [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/cln6
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