HTR5A-AS1

HTR5A antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 7:155067034-155072450

Previous symbols: [ "HTR5AOS" ]

Links

ENSG00000220575 ∙ NCBI:100128264 ∙ ∙ HGNC:48956 ∙ ∙ ∙ 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 HTR5A-AS1 gene.

• Inborn genetic diseases (8 variants)
• not provided (3 variants)
• Malignant tumor of prostate (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR5A-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			9		3	12
Total	0	0	9	0	3

Variants in HTR5A-AS1

This is a list of pathogenic ClinVar variants found in the HTR5A-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
7-155070967-G-C		not specified	Uncertain significance (Jan 09, 2024)
7-155070978-G-C		Malignant tumor of prostate	Uncertain significance (-)
7-155071009-C-T		not specified	Uncertain significance (Jul 30, 2023)
7-155071020-G-A		not specified	Uncertain significance (Mar 29, 2022)
7-155071080-G-T		not specified	Uncertain significance (Mar 01, 2023)
7-155071089-A-G		not specified	Uncertain significance (Jan 19, 2024)
7-155071104-C-G		not specified	Uncertain significance (Jun 22, 2021)
7-155071199-C-T			Benign (Dec 31, 2019)
7-155071297-C-T		not specified	Uncertain significance (Jun 01, 2023)
7-155071383-A-G		not specified	Uncertain significance (Jul 15, 2021)
7-155071466-C-T			Benign (Dec 31, 2019)
7-155071520-C-T			Benign (Mar 05, 2018)
7-155071565-G-C		not specified	Uncertain significance (Jan 19, 2024)
7-155071583-G-T		not specified	Uncertain significance (Aug 02, 2022)
7-155071629-G-A		not specified	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR5A-AS1	protein_coding	protein_coding	ENST00000543018	3	4491

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000913	0.352	124917	0	4	124921	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.302	86	94.2	0.912	0.00000613	953
Missense in Polyphen		1	3.0028	0.33303		22
Synonymous	0.694	37	42.8	0.865	0.00000311	310
Loss of Function	-0.0261	6	5.93	1.01	3.46e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.296
• ghis: 0.551

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium