HOTTIP

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

Basic information

Region (hg38): 7:27198575-27207259

Previous symbols: [ "NCRNA00213" ]

Links

ENSG00000243766 ∙ NCBI:100316868 ∙ OMIM:614060 ∙ HGNC:37461 ∙ ∙ ∙ 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 HOTTIP gene.

• not provided (70 variants)
• Inborn genetic diseases (24 variants)
• Hand-foot-genital syndrome (7 variants)
• Guttmacher syndrome;Hand-foot-genital syndrome (7 variants)
• not specified (5 variants)
• Hand-foot-genital syndrome;Guttmacher syndrome (3 variants)
• HOXA13-related condition (1 variants)
• - (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOTTIP 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)		1				1
splice region						0
non coding	4	2	54	32	10	102
Total	4	3	54	32	10

Variants in HOTTIP

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

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

Position	Type	Phenotype	Significance	ClinVar
7-27199072-C-G			Benign (Nov 12, 2018)
7-27199143-G-A			Benign (Apr 17, 2023)
7-27199157-G-C			Uncertain significance (May 22, 2023)
7-27199181-G-A			Benign (Nov 13, 2023)
7-27199191-G-T		Inborn genetic diseases	Uncertain significance (Jun 07, 2023)
7-27199194-T-G		Hand-foot-genital syndrome	Uncertain significance (-)
7-27199207-A-G		Inborn genetic diseases	Uncertain significance (Nov 03, 2023)
7-27199208-G-A			Likely benign (Jun 13, 2022)
7-27199209-T-G		Hand-foot-genital syndrome	Likely pathogenic (Oct 03, 2022)
7-27199228-C-T			Uncertain significance (Dec 30, 2021)
7-27199229-G-A		HOXA13-related disorder	Likely benign (Jun 21, 2019)
7-27199230-T-C		Inborn genetic diseases	Uncertain significance (Nov 10, 2022)
7-27199294-C-A		Inborn genetic diseases	Uncertain significance (Mar 01, 2023)
7-27199294-C-T			Uncertain significance (May 14, 2022)
7-27199336-C-CA		Hand-foot-genital syndrome	Likely pathogenic (May 21, 2020)
7-27199400-C-T			Likely benign (Aug 09, 2022)
7-27199416-A-T		Inborn genetic diseases	Uncertain significance (Aug 21, 2023)
7-27199426-C-T		HOXA13-related disorder	Uncertain significance (May 28, 2024)
7-27199434-C-T		Inborn genetic diseases	Uncertain significance (Feb 14, 2023)
7-27199445-C-A			Benign/Likely benign (Jan 22, 2024)
7-27199447-T-A		Inborn genetic diseases	Uncertain significance (Jun 23, 2021)
7-27199462-AGGCGGC-A			Uncertain significance (Oct 24, 2022)
7-27199462-A-AGGC			Likely benign (Sep 07, 2022)
7-27199464-G-A		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
7-27199475-G-A		not specified	Uncertain significance (Feb 14, 2020)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Mouse Genome Informatics

• Gene name: Hottip
• Phenotype: muscle phenotype; normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype