LINC01500

long intergenic non-protein coding RNA 1500, the group of Long intergenic non-protein coding RNAs

Basic information

Region (hg38): 14:58646631-59184247

Links

ENSG00000258583 ∙ NCBI:102723742 ∙ ∙ HGNC:51166 ∙ ∙ ∙ 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 LINC01500 gene.

• Inborn genetic diseases (11 variants)
• not provided (8 variants)
• Townes-Brocks syndrome 2 (3 variants)
• Rieger anomaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINC01500 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	1		14	5	3	23
Total	1	0	14	5	3

Variants in LINC01500

This is a list of pathogenic ClinVar variants found in the LINC01500 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-58646633-G-C		Rieger anomaly	Likely benign (Jan 01, 2013)
14-58646653-G-A		not specified	Uncertain significance (May 30, 2023)
14-58646658-T-C			Likely benign (Dec 31, 2019)
14-58646682-T-C		DACT1-related disorder • not specified	Conflicting classifications of pathogenicity (Dec 13, 2023)
14-58646686-A-G		not specified	Uncertain significance (Jan 31, 2022)
14-58646692-C-T		not specified	Uncertain significance (May 12, 2024)
14-58646711-C-T		DACT1-related disorder	Likely benign (Mar 22, 2019)
14-58646712-G-A		DACT1-related disorder	Benign (Mar 13, 2019)
14-58646731-G-A		not specified	Uncertain significance (Dec 19, 2023)
14-58646743-C-T			Uncertain significance (Sep 01, 2022)
14-58646751-C-T		not specified	Uncertain significance (Feb 16, 2023)
14-58646758-C-T		not specified	Uncertain significance (Feb 22, 2023)
14-58646760-T-A			Likely benign (Jul 02, 2018)
14-58646763-G-T		DACT1-related disorder	Uncertain significance (Mar 24, 2024)
14-58646769-C-T		not specified	Uncertain significance (Sep 20, 2023)
14-58646775-G-A		not specified	Uncertain significance (Jan 10, 2022)
14-58646812-G-A		not specified	Uncertain significance (Apr 06, 2024)
14-58646818-C-A		not specified	Uncertain significance (Jun 22, 2023)
14-58646844-A-T		not specified	Uncertain significance (May 24, 2023)
14-58646855-C-T		DACT1-related disorder	Benign (Jul 13, 2018)
14-58646856-G-A		Townes-Brocks syndrome 2	Uncertain significance (Apr 28, 2022)
14-58646874-A-G		not specified	Uncertain significance (Sep 01, 2021)
14-58646877-A-G		not specified	Uncertain significance (Aug 30, 2021)
14-58646882-C-T			Benign (Dec 31, 2019)
14-58646903-T-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP