ATP1A1-AS1

ATP1A1 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 1:116378437-116421301

Previous symbols: [ "C1orf203", "ATP1A1OS" ]

Links

ENSG00000203865 ∙ NCBI:84852 ∙ OMIM:618305 ∙ HGNC:28262 ∙ Uniprot:Q5TC04 ∙ AlphaFold ∙ 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 ATP1A1-AS1 gene.

• not provided (456 variants)
• Charcot-marie-tooth disease, axonal, type 2DD (26 variants)
• Hypomagnesemia, seizures, and intellectual disability 2 (21 variants)
• Inborn genetic diseases (20 variants)
• Charcot-Marie-Tooth disease type 2A2 (7 variants)
• Aldosterone-producing adrenal cortex adenoma (3 variants)
• Marfanoid habitus and intellectual disability (2 variants)
• Malignant tumor of prostate (1 variants)
• Intellectual disability (1 variants)
• Charcot-marie-tooth disease, axonal, type 2DD;Hypomagnesemia, seizures, and intellectual disability 2 (1 variants)
• ATP1A1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP1A1-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)			2	4		6
splice region						0
non coding	12	7	156	260	48	483
Total	12	7	158	264	48

Variants in ATP1A1-AS1

This is a list of pathogenic ClinVar variants found in the ATP1A1-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
1-116383811-G-A			Benign (May 11, 2021)
1-116383998-C-G			Likely benign (Mar 23, 2021)
1-116384003-T-C			Likely benign (Sep 24, 2022)
1-116384010-A-G			Likely benign (Sep 06, 2022)
1-116384014-G-A			Uncertain significance (Jul 10, 2023)
1-116384014-G-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 15, 2023)
1-116384015-T-C		Inborn genetic diseases	Uncertain significance (Oct 27, 2023)
1-116384019-A-T			Likely benign (Sep 28, 2022)
1-116384020-C-T		Inborn genetic diseases	Uncertain significance (Apr 08, 2023)
1-116384021-G-A			Uncertain significance (May 24, 2023)
1-116384021-G-T			Uncertain significance (Mar 01, 2023)
1-116384026-A-C			Uncertain significance (Jul 27, 2023)
1-116384034-G-T			Uncertain significance (Dec 27, 2023)
1-116384035-C-T			Uncertain significance (Nov 16, 2023)
1-116384037-T-C			Likely benign (Dec 20, 2023)
1-116384039-C-A			Uncertain significance (Dec 17, 2023)
1-116384040-A-G			Benign/Likely benign (Feb 01, 2024)
1-116384043-T-C			Likely benign (Jul 13, 2023)
1-116384049-A-G			Likely benign (Jan 31, 2023)
1-116384054-A-G		ATP1A1-related disorder	Uncertain significance (Jul 06, 2022)
1-116384061-T-C			Benign (May 03, 2022)
1-116384061-TAAAAAGGGC-T			Uncertain significance (Oct 16, 2023)
1-116384061-T-TAAAAAGGGC			Uncertain significance (Jan 05, 2024)
1-116384063-A-G			Uncertain significance (Oct 25, 2022)
1-116384067-G-A			Likely benign (Dec 27, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.510