FXYD4

FXYD domain containing ion transport regulator 4

Basic information

Region (hg38): 10:43371636-43376335

Links

ENSG00000150201 ∙ NCBI:53828 ∙ OMIM:616926 ∙ HGNC:4028 ∙ Uniprot:P59646 ∙ 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 FXYD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FXYD4 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in FXYD4

This is a list of pathogenic ClinVar variants found in the FXYD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-43373780-G-A		not specified	Uncertain significance (Feb 05, 2025)
10-43374487-G-A		not specified	Uncertain significance (Feb 05, 2024)
10-43374495-C-G		not specified	Uncertain significance (Oct 25, 2023)
10-43374624-G-T		not specified	Uncertain significance (Dec 08, 2023)
10-43374627-C-T		not specified	Uncertain significance (Oct 07, 2024)
10-43374634-A-G		not specified	Uncertain significance (Oct 14, 2023)
10-43375559-T-C		not specified	Uncertain significance (Dec 16, 2024)
10-43375561-G-C		not specified	Uncertain significance (Feb 05, 2025)
10-43375715-A-G		not specified	Uncertain significance (Nov 10, 2023)
10-43375716-G-A		not specified	Uncertain significance (Oct 24, 2024)
10-43375730-C-T		not specified	Uncertain significance (Jan 22, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FXYD4	protein_coding	protein_coding	ENST00000476166	7	4694

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000316	0.600	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.303	52	46.2	1.13	0.00000246	566
Missense in Polyphen		9	6.6592	1.3515		67
Synonymous	-0.273	21	19.5	1.08	0.00000129	168
Loss of Function	0.605	6	7.83	0.767	3.43e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000366	0.000365
Ashkenazi Jewish	0.000595	0.000595
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Aldosterone-regulated sodium reabsorption - Homo sapiens (human);Ion channel transport;Ion homeostasis;Transport of small molecules;Cardiac conduction;Muscle contraction;Ion transport by P-type ATPases (Consensus)

Intolerance Scores

• loftool: 0.713
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.204

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fxyd4
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: potassium ion transmembrane transport;regulation of sodium ion transmembrane transporter activity
• Cellular component: plasma membrane;sodium:potassium-exchanging ATPase complex
• Molecular function: potassium channel activity;sodium channel regulator activity;ATPase binding;ion channel regulator activity