ATP2A1-AS1

ATP2A1 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 16:28877938-28879950

Links

ENSG00000260442 ∙ NCBI:100289092 ∙ ∙ HGNC:51370 ∙ ∙ ∙ 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 ATP2A1-AS1 gene.

• Brody myopathy (55 variants)
• not provided (12 variants)
• not specified (5 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP2A1-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)	1		1	6		8
splice region						0
non coding	4	3	25	17	7	56
Total	5	3	26	23	7

Highest pathogenic variant AF is 0.0000197

Variants in ATP2A1-AS1

This is a list of pathogenic ClinVar variants found in the ATP2A1-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
16-28878165-C-A			Benign (Jun 16, 2018)
16-28878376-C-CT			Benign (Nov 14, 2019)
16-28878386-CA-C			Benign (Jun 14, 2018)
16-28878650-C-T		not specified • Brody myopathy	Benign (Jan 12, 2018)
16-28878657-C-T		Brody myopathy	Uncertain significance (Jan 13, 2018)
16-28878660-G-A		not specified • Brody myopathy	Likely benign (Jan 13, 2018)
16-28878665-G-A		not specified	Likely benign (Jan 08, 2018)
16-28878670-C-T			Uncertain significance (Feb 10, 2021)
16-28878672-A-G		Brody myopathy	Uncertain significance (Aug 04, 2022)
16-28878675-G-A		Brody myopathy	Uncertain significance (May 24, 2022)
16-28878677-G-A		Brody myopathy	Likely benign (May 23, 2023)
16-28878680-C-T		Brody myopathy	Likely benign (May 09, 2023)
16-28878712-C-A		Brody myopathy	Uncertain significance (Jan 12, 2018)
16-28878715-A-G		Brody myopathy	Uncertain significance (Jun 18, 2022)
16-28878722-GGTGA-G		Brody myopathy	Pathogenic (Nov 13, 2023)
16-28878726-A-G		Brody myopathy	Uncertain significance (Sep 01, 2021)
16-28878729-G-A		Brody myopathy	Uncertain significance (May 23, 2022)
16-28878737-G-A		Brody myopathy	Likely benign (Dec 02, 2022)
16-28878749-G-A		Brody myopathy	Uncertain significance (Jan 13, 2018)
16-28878752-C-G		Brody myopathy	Uncertain significance (Nov 27, 2023)
16-28878759-A-C		Brody myopathy	Uncertain significance (Sep 24, 2021)
16-28878763-G-A		Brody myopathy	Uncertain significance (Oct 25, 2022)
16-28878769-T-A		Brody myopathy	Uncertain significance (Dec 09, 2021)
16-28878771-G-T		Brody myopathy • ATP2A1-related disorder	Conflicting classifications of pathogenicity (Nov 28, 2023)
16-28878780-G-A		Brody myopathy • Inborn genetic diseases	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP