ATP1B4

ATPase Na+/K+ transporting family member beta 4

Basic information

Region (hg38): X:120362084-120383249

Links

ENSG00000101892 ∙ NCBI:23439 ∙ OMIM:301073 ∙ HGNC:808 ∙ Uniprot:Q9UN42 ∙ 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 ATP1B4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP1B4 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				3		3
missense			21			21
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	4	0

Variants in ATP1B4

This is a list of pathogenic ClinVar variants found in the ATP1B4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-120362221-G-A		not specified	Uncertain significance (Sep 14, 2022)
X-120366532-C-T		not specified	Uncertain significance (Dec 16, 2023)
X-120366591-C-T		not specified	Uncertain significance (Aug 08, 2023)
X-120366592-G-A		not specified	Likely benign (Jun 16, 2024)
X-120366594-G-A		not specified	Uncertain significance (Apr 19, 2023)
X-120366603-G-A		not specified	Uncertain significance (Jun 12, 2023)
X-120366670-A-G		not specified	Uncertain significance (Jun 02, 2024)
X-120366784-G-A		not specified	Uncertain significance (Apr 04, 2024)
X-120370759-G-C		not specified	Uncertain significance (Jun 23, 2023)
X-120370814-C-G		not specified	Uncertain significance (Dec 15, 2023)
X-120371125-C-G		not specified	Uncertain significance (Jul 25, 2023)
X-120371153-G-A		not specified	Uncertain significance (Jan 30, 2024)
X-120371186-A-T		not specified	Uncertain significance (Jan 09, 2024)
X-120375382-C-G		not specified	Uncertain significance (Dec 13, 2023)
X-120375418-G-C			Likely benign (Aug 01, 2022)
X-120375464-G-T		not specified	Uncertain significance (Jan 16, 2024)
X-120375479-C-T		not specified	Uncertain significance (Dec 27, 2023)
X-120375515-C-T		not specified	Uncertain significance (Dec 14, 2023)
X-120375516-C-G		not specified	Uncertain significance (Dec 19, 2022)
X-120375563-A-G		not specified	Uncertain significance (Oct 03, 2022)
X-120376413-G-C		not specified	Uncertain significance (Aug 08, 2023)
X-120378699-C-T			Likely benign (Dec 01, 2022)
X-120378724-C-T		not specified	Uncertain significance (Jun 24, 2022)
X-120378725-G-A			Likely benign (Mar 01, 2023)
X-120379539-G-C		not specified	Uncertain significance (Feb 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP1B4	protein_coding	protein_coding	ENST00000218008	8	20260

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000356	0.957	125703	7	13	125723	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.224	136	144	0.947	0.0000113	2371
Missense in Polyphen		51	55.897	0.9124		987
Synonymous	-1.18	65	54.0	1.20	0.00000442	645
Loss of Function	1.80	8	15.7	0.509	0.00000131	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000294	0.000294
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000106	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a transcriptional coregulator during muscle development through its interaction with SNW1. Has lost its ancestral function as a Na,K-ATPase beta-subunit. {ECO:0000269|PubMed:17592128}.
• Pathway: Aldosterone synthesis and secretion - Homo sapiens (human);Cardiac muscle contraction - Homo sapiens (human);Thyroid hormone synthesis - Homo sapiens (human);Protein digestion and absorption - Homo sapiens (human);Bile secretion - Homo sapiens (human);Carbohydrate digestion and absorption - Homo sapiens (human);Gastric acid secretion - Homo sapiens (human);Proximal tubule bicarbonate reclamation - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human);Aldosterone-regulated sodium reabsorption - Homo sapiens (human);Salivary secretion - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Mineral absorption - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Insulin secretion - Homo sapiens (human);Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Purine metabolism;SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.812
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.178
• hipred: N
• hipred_score: 0.287
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.159

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp1b4

Gene ontology

• Biological process: regulation of transcription, DNA-templated;monovalent inorganic cation transport;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nuclear envelope;nuclear inner membrane;integral component of plasma membrane;sodium:potassium-exchanging ATPase complex
• Molecular function: protein binding;monovalent inorganic cation transmembrane transporter activity