USH2A-AS2

USH2A antisense RNA 2, the group of Antisense RNAs

Basic information

Region (hg38): 1:216072454-216086917

Links

ENSG00000233620 ∙ NCBI:102723833 ∙ ∙ HGNC:40605 ∙ ∙ ∙ 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 USH2A-AS2 gene.

• not provided (410 variants)
• Usher syndrome type 2A (103 variants)
• Retinitis pigmentosa 39 (91 variants)
• not specified (35 variants)
• Retinal dystrophy (21 variants)
• Retinitis pigmentosa 39;Usher syndrome type 2A (16 variants)
• Retinitis pigmentosa (14 variants)
• Usher syndrome type 2A;Retinitis pigmentosa 39 (13 variants)
• Inborn genetic diseases (12 variants)
• Usher syndrome (11 variants)
• Rare genetic deafness (5 variants)
• Usher syndrome type 2 (4 variants)
• USH2A-related condition (3 variants)
• Hearing impairment (2 variants)
• USH2A-Related Disorders (2 variants)
• 13 conditions (1 variants)
• Autosomal recessive retinitis pigmentosa (1 variants)
• Childhood onset hearing loss (1 variants)
• Malignant tumor of prostate (1 variants)
• Sensorineural hearing impairment (1 variants)
• Leber congenital amaurosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USH2A-AS2 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)	2	3	3	4		12
splice region						0
non coding	54	48	148	166	22	438
Total	56	51	151	170	22

Highest pathogenic variant AF is 0.0000263

Variants in USH2A-AS2

This is a list of pathogenic ClinVar variants found in the USH2A-AS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-216072702-G-A			Benign (Jul 07, 2018)
1-216072773-T-C			Likely benign (Apr 20, 2019)
1-216072872-T-G		not specified • Usher syndrome type 2A • Retinitis pigmentosa 39	Benign (Jan 31, 2024)
1-216072875-A-G			Likely benign (Jan 17, 2023)
1-216072879-A-G			Likely benign (Jan 11, 2024)
1-216072882-T-A			Likely benign (Aug 30, 2022)
1-216072887-A-G		Rare genetic deafness • USH2A-related disorder • Retinitis pigmentosa 39 • Usher syndrome • Retinal dystrophy • Usher syndrome type 2A	Likely pathogenic (Oct 29, 2019)
1-216072887-AC-A			Pathogenic (Aug 07, 2022)
1-216072888-C-G		Retinal dystrophy • Retinitis pigmentosa 39	Pathogenic/Likely pathogenic (Oct 02, 2023)
1-216072890-T-C			Uncertain significance (Aug 11, 2020)
1-216072891-G-A		not specified • Usher syndrome type 2A • Retinitis pigmentosa 39 • Inborn genetic diseases	Uncertain significance (Nov 04, 2023)
1-216072893-T-G			Likely benign (Aug 12, 2022)
1-216072896-T-A			Likely benign (Dec 11, 2023)
1-216072896-T-C			Likely benign (Nov 05, 2023)
1-216072898-T-C			Uncertain significance (Nov 22, 2022)
1-216072899-T-C			Likely benign (Oct 17, 2023)
1-216072901-T-C		Inborn genetic diseases	Uncertain significance (Mar 01, 2024)
1-216072902-A-G		not specified • Usher syndrome type 2A;Retinitis pigmentosa 39 • Usher syndrome type 2A • Retinitis pigmentosa 39	Benign/Likely benign (Jan 19, 2024)
1-216072903-C-T			Uncertain significance (Aug 31, 2022)
1-216072904-G-A		Usher syndrome type 2A • Inborn genetic diseases • Retinitis pigmentosa 39	Uncertain significance (Nov 04, 2023)
1-216072904-G-T			Uncertain significance (Jun 09, 2022)
1-216072909-C-A		Malignant tumor of prostate	Uncertain significance (-)
1-216072909-C-T		Retinal dystrophy	Uncertain significance (Oct 01, 2023)
1-216072910-G-A		Usher syndrome type 2A • Retinal dystrophy • Retinitis pigmentosa 39	Pathogenic (Dec 24, 2023)
1-216072909-C-CGA		Retinitis pigmentosa 39	Pathogenic (Jun 13, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP