USH2A-AS1

USH2A antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 1:216194051-216238122

Links

ENSG00000236292 ∙ NCBI:105372918 ∙ ∙ HGNC:40606 ∙ ∙ ∙ 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-AS1 gene.

• not provided (335 variants)
• Usher syndrome type 2A (109 variants)
• Retinitis pigmentosa 39 (80 variants)
• not specified (30 variants)
• Retinitis pigmentosa (28 variants)
• Retinitis pigmentosa 39;Usher syndrome type 2A (18 variants)
• Retinal dystrophy (17 variants)
• Usher syndrome (15 variants)
• Inborn genetic diseases (13 variants)
• Usher syndrome type 2A;Retinitis pigmentosa 39 (10 variants)
• Rare genetic deafness (6 variants)
• Usher syndrome type 2 (4 variants)
• USH2A-Related Disorders (2 variants)
• Deafness (1 variants)
• Hearing loss, autosomal recessive (1 variants)
• Usher syndrome type 1 (1 variants)
• Retinitis Pigmentosa, Recessive (1 variants)
• - (1 variants)
• Autosomal recessive retinitis pigmentosa (1 variants)
• Retinitis pigmentosa-deafness syndrome (1 variants)
• Cone/cone-rod dystrophy (1 variants)
• Pigmentary retinopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USH2A-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	56	60	127	137	12	392
Total	56	60	127	137	12

Highest pathogenic variant AF is 0.00000662

Variants in USH2A-AS1

This is a list of pathogenic ClinVar variants found in the USH2A-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
1-216196495-AT-A			Benign (Jul 17, 2018)
1-216196532-AT-A			Likely benign (Jan 16, 2024)
1-216196536-G-T			Likely benign (Nov 27, 2023)
1-216196541-A-C			Likely benign (Jan 18, 2024)
1-216196544-T-C			Likely benign (Jan 11, 2024)
1-216196550-T-C		Retinitis pigmentosa 39 • Usher syndrome type 2A	Uncertain significance (Apr 11, 2023)
1-216196551-AC-A		Usher syndrome • Retinitis pigmentosa 39 • Usher syndrome type 2A	Pathogenic/Likely pathogenic (Apr 11, 2023)
1-216196552-C-A		Retinitis pigmentosa 39	Pathogenic/Likely pathogenic (Jan 19, 2024)
1-216196552-C-T		Retinal dystrophy • Usher syndrome type 2A	Likely pathogenic (May 06, 2024)
1-216196553-C-A		Usher syndrome type 2A • Retinitis pigmentosa 39 • not specified	Conflicting classifications of pathogenicity (Jun 12, 2024)
1-216196555-G-A			Pathogenic (Aug 23, 2023)
1-216196555-G-C			Uncertain significance (Aug 21, 2022)
1-216196556-T-G			Likely benign (Mar 09, 2022)
1-216196557-G-GA			Pathogenic (Sep 17, 2023)
1-216196559-A-G			Likely benign (Apr 04, 2023)
1-216196561-A-G			Uncertain significance (Oct 09, 2023)
1-216196562-C-T			Likely benign (Jan 29, 2024)
1-216196563-G-A		Retinal dystrophy	Uncertain significance (Oct 01, 2023)
1-216196567-T-C			Uncertain significance (Nov 18, 2021)
1-216196571-A-G			Likely benign (Sep 27, 2023)
1-216196571-A-T			Likely benign (Jan 29, 2024)
1-216196573-T-A			Uncertain significance (Aug 31, 2021)
1-216196573-T-C		Retinal dystrophy	Uncertain significance (Oct 01, 2023)
1-216196577-C-T			Likely benign (Nov 25, 2023)
1-216196579-G-A		Retinitis pigmentosa 39	Likely pathogenic (Jan 05, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP