CTNS-AS1

CTNS antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 17:3655621-3658092

Links

ENSG00000262903 ∙ NCBI:105371492 ∙ ∙ HGNC:56090 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CTNS-AS1 gene.

• Ocular cystinosis;Juvenile nephropathic cystinosis;Inborn genetic diseases (73 variants)
• Nephropathic cystinosis (49 variants)
• Inborn genetic diseases;Ocular cystinosis;Juvenile nephropathic cystinosis (46 variants)
• Cystinosis (28 variants)
• not provided (21 variants)
• Ocular cystinosis (13 variants)
• Ocular cystinosis;Juvenile nephropathic cystinosis;Nephropathic cystinosis (13 variants)
• Nephropathic cystinosis;Ocular cystinosis;Juvenile nephropathic cystinosis (10 variants)
• not specified (9 variants)
• Inborn genetic diseases (8 variants)
• Ocular cystinosis;Nephropathic cystinosis;Juvenile nephropathic cystinosis (3 variants)
• Juvenile nephropathic cystinosis;Inborn genetic diseases;Ocular cystinosis (2 variants)
• Juvenile nephropathic cystinosis;Ocular cystinosis;Inborn genetic diseases (1 variants)
• Infantile nephropathic cystinosis (1 variants)
• See cases (1 variants)
• Juvenile nephropathic cystinosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTNS-AS1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	16	27	31	82	6	162
Total	16	27	31	82	6

Highest pathogenic variant AF is 0.0000395

Variants in CTNS-AS1

This is a list of pathogenic ClinVar variants found in the CTNS-AS1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-3655669-C-A			Benign (Dec 31, 2018)
17-3656389-CTGCCCCTCCACCCCCGCCAGTCCTCACCCTCTGCCCTGTCCCTCCACCCCTGCCAGTCTTCACCCCCTGCCCTGTCT-C		Ocular cystinosis;Juvenile nephropathic cystinosis;Inborn genetic diseases	Likely benign (Aug 13, 2023)
17-3656425-CTGTCCCTCCACCCCTGCCAGTCTTCACCCCCTGCCCTGTCT-C		Juvenile nephropathic cystinosis;Inborn genetic diseases;Ocular cystinosis	Likely benign (Aug 03, 2023)
17-3656449-TCACCCCCTGCCCTGTCTTGTCCCTC-T		Nephropathic cystinosis	Uncertain significance (Apr 03, 2018)
17-3656470-C-T		Juvenile nephropathic cystinosis;Inborn genetic diseases;Ocular cystinosis	Likely benign (Jan 25, 2024)
17-3656475-C-T		Juvenile nephropathic cystinosis;Inborn genetic diseases;Ocular cystinosis	Likely benign (Mar 17, 2024)
17-3656477-C-A		Ocular cystinosis;Inborn genetic diseases;Juvenile nephropathic cystinosis	Likely benign (Oct 17, 2023)
17-3656477-C-T		Juvenile nephropathic cystinosis • Inborn genetic diseases;Ocular cystinosis;Juvenile nephropathic cystinosis	Likely benign (Nov 24, 2023)
17-3656478-C-T		Inborn genetic diseases;Ocular cystinosis;Juvenile nephropathic cystinosis	Likely benign (Oct 17, 2023)
17-3656479-C-A		Juvenile nephropathic cystinosis;Inborn genetic diseases;Ocular cystinosis	Likely benign (Feb 06, 2024)
17-3656480-C-A		Ocular cystinosis • not specified • Nephropathic cystinosis • Cystinosis • Inborn genetic diseases;Ocular cystinosis;Juvenile nephropathic cystinosis • CTNS-related disorder	Benign/Likely benign (Jan 31, 2025)
17-3656481-C-T		Inborn genetic diseases;Ocular cystinosis;Juvenile nephropathic cystinosis	Likely benign (Feb 14, 2023)
17-3656485-A-C		Nephropathic cystinosis	Pathogenic (Jul 14, 2024)
17-3656486-G-A		Nephropathic cystinosis	Likely pathogenic (Feb 27, 2024)
17-3656487-T-C		not specified • Ocular cystinosis • Nephropathic cystinosis • Ocular cystinosis;Juvenile nephropathic cystinosis;Inborn genetic diseases • Cystinosis	Benign (Feb 03, 2025)
17-3656490-C-T		Ocular cystinosis;Juvenile nephropathic cystinosis;Inborn genetic diseases	Likely benign (Apr 29, 2022)
17-3656498-T-C		Nephropathic cystinosis • Cystinosis • CTNS-related disorder • Inborn genetic diseases;Ocular cystinosis;Juvenile nephropathic cystinosis • Nephropathic cystinosis;Ocular cystinosis;Juvenile nephropathic cystinosis	Pathogenic/Likely pathogenic (Mar 21, 2024)
17-3656499-G-A		Inborn genetic diseases;Ocular cystinosis;Juvenile nephropathic cystinosis	Likely benign (Sep 27, 2023)
17-3656502-C-T		Inborn genetic diseases;Ocular cystinosis;Juvenile nephropathic cystinosis	Likely benign (Jan 23, 2020)
17-3656502-CT-C		Nephropathic cystinosis	Pathogenic (Jun 28, 2019)
17-3656505-C-T		not specified • Ocular cystinosis • Cystinosis • Ocular cystinosis;Juvenile nephropathic cystinosis;Inborn genetic diseases • Nephropathic cystinosis	Conflicting classifications of pathogenicity (Dec 23, 2024)
17-3656506-G-A		Nephropathic cystinosis • Ocular cystinosis • Juvenile nephropathic cystinosis;Ocular cystinosis;Nephropathic cystinosis	Uncertain significance (Apr 30, 2024)
17-3656510-TC-T		Nephropathic cystinosis	Likely pathogenic (Feb 26, 2024)
17-3656511-C-T		Inborn genetic diseases;Ocular cystinosis;Juvenile nephropathic cystinosis	Likely benign (Oct 09, 2023)
17-3656512-G-A		Ocular cystinosis;Juvenile nephropathic cystinosis;Inborn genetic diseases	Likely benign (May 06, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP