HOTAIRM1

HOXA transcript antisense RNA, myeloid-specific 1, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 7:27095647-27100265

Links

ENSG00000233429 ∙ NCBI:100506311 ∙ ∙ HGNC:37117 ∙ ∙ ∙ 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 HOTAIRM1 gene.

• Inborn genetic diseases (20 variants)
• Human HOXA1 syndromes (12 variants)
• Bosley-Salih-Alorainy syndrome (11 variants)
• not provided (10 variants)
• Bilateral microtia-deafness-cleft palate syndrome (3 variants)
• not specified (2 variants)
• Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOTAIRM1 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	4		19	13	4	40
Total	4	0	19	13	4

Highest pathogenic variant AF is 0.00000657

Variants in HOTAIRM1

This is a list of pathogenic ClinVar variants found in the HOTAIRM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-27095658-G-C		Bosley-Salih-Alorainy syndrome	Uncertain significance (Jun 14, 2016)
7-27095665-G-A		Inborn genetic diseases	Uncertain significance (Jan 04, 2022)
7-27095665-G-C		Inborn genetic diseases	Uncertain significance (Dec 07, 2023)
7-27095689-GGGTGGCGAT-G		not specified	Benign (Jun 01, 2022)
7-27095691-GTGGCGA-G		HOXA1-related disorder	Likely benign (Jul 30, 2023)
7-27095694-GCGA-G		Bilateral microtia-deafness-cleft palate syndrome	Likely benign (Jun 14, 2016)
7-27095695-C-T		Bilateral microtia-deafness-cleft palate syndrome	Benign (Jun 14, 2016)
7-27095695-C-C			Benign (Jan 18, 2024)
7-27095697-A-G		Human HOXA1 syndromes • Bosley-Salih-Alorainy syndrome • Inborn genetic diseases	Conflicting classifications of pathogenicity (Mar 09, 2018)
7-27095697-ATGG-A		not specified • Inborn genetic diseases	Likely benign (Mar 13, 2019)
7-27095697-ATGGTGG-A		Inborn genetic diseases	Likely benign (Nov 04, 2016)
7-27095697-ATGGTGGTGG-A		Inborn genetic diseases	Benign (Dec 31, 2019)
7-27095698-T-G			not provided (-)
7-27095697-A-ATGG		Inborn genetic diseases	Benign/Likely benign (Dec 31, 2019)
7-27095697-A-ATGGTGG		Inborn genetic diseases • HOXA1-related disorder	Likely benign (Mar 21, 2018)
7-27095697-A-ATGGTGGTGG		Inborn genetic diseases	Likely benign (Nov 30, 2017)
7-27095700-G-A		Bosley-Salih-Alorainy syndrome • Bilateral microtia-deafness-cleft palate syndrome • Human HOXA1 syndromes • Inborn genetic diseases • HOXA1-related disorder	Benign/Likely benign (Jun 14, 2016)
7-27095702-G-A		Inborn genetic diseases	Uncertain significance (Mar 20, 2024)
7-27095703-G-A		Human HOXA1 syndromes	Uncertain significance (Jan 12, 2018)
7-27095706-G-A		Bosley-Salih-Alorainy syndrome • Inborn genetic diseases • HOXA1-related disorder	Conflicting classifications of pathogenicity (Apr 28, 2017)
7-27095717-G-A		Bosley-Salih-Alorainy syndrome • Inborn genetic diseases	Uncertain significance (Nov 13, 2020)
7-27095719-T-G		Inborn genetic diseases • Bosley-Salih-Alorainy syndrome	Conflicting classifications of pathogenicity (Nov 10, 2018)
7-27095725-G-A		Inborn genetic diseases	Uncertain significance (Jul 15, 2021)
7-27095727-AC-A		Bosley-Salih-Alorainy syndrome	Pathogenic (May 15, 2008)
7-27095733-C-A		Inborn genetic diseases	Uncertain significance (Jun 05, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Mouse Genome Informatics

• Gene name: Hotairm1