HOTAIR

HOX transcript antisense RNA, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 12:53962308-53975055

Links

ENSG00000228630 ∙ NCBI:100124700 ∙ OMIM:611400 ∙ HGNC:33510 ∙ ∙ ∙ 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 HOTAIR gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOTAIR 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			10	1		11
Total	0	0	10	1	0

Variants in HOTAIR

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

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

Position	Type	Phenotype	Significance	ClinVar
12-53973311-G-C		not specified	Uncertain significance (Dec 08, 2023)
12-53973334-C-A		not specified	Uncertain significance (Jan 30, 2024)
12-53973339-A-G		not specified	Uncertain significance (Mar 25, 2024)
12-53973432-C-T		not specified	Uncertain significance (Apr 17, 2023)
12-53973449-G-A		not specified	Uncertain significance (Feb 27, 2024)
12-53973519-A-G		not specified	Uncertain significance (May 17, 2023)
12-53973600-C-T		not specified	Uncertain significance (Jan 17, 2024)
12-53973615-A-G		not specified	Uncertain significance (Sep 25, 2023)
12-53973617-C-A		not specified	Uncertain significance (Jun 30, 2023)
12-53973645-C-G		not specified	Uncertain significance (Oct 26, 2022)
12-53973647-G-T		not specified	Uncertain significance (Dec 28, 2022)
12-53973728-G-C		not specified	Uncertain significance (Nov 10, 2022)
12-53973743-G-A		not specified	Uncertain significance (Feb 06, 2023)
12-53973764-G-A		not specified	Uncertain significance (Nov 12, 2021)
12-53973782-C-T		not specified	Uncertain significance (Dec 20, 2022)
12-53973810-C-G		not specified	Likely benign (Jun 11, 2021)
12-53973815-C-G		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Pathway: LncRNA-mediated mechanisms of therapeutic resistance (Consensus)

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Mouse Genome Informatics

• Gene name: Hotair
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype