FXYD1

FXYD domain containing ion transport regulator 1

Basic information

Region (hg38): 19:35138824-35143109

Previous symbols: [ "PLM" ]

Links

ENSG00000266964

∙ NCBI:5348 ∙ OMIM:602359 ∙ HGNC:4025 ∙ Uniprot:O00168 ∙ 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 FXYD1 gene.

not_specified (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FXYD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021902.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			9 clinvar			9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	9	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FXYD1	protein_coding	protein_coding	ENST00000588081	6	4302

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.244	0.729	125691	0	9	125700	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.525	44	55.0	0.801	0.00000285	589
Missense in Polyphen		12	19.604	0.61211		221
Synonymous	-0.977	28	22.1	1.26	0.00000130	175
Loss of Function	1.85	2	7.44	0.269	3.25e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Associates with and regulates the activity of the sodium/potassium-transporting ATPase (NKA) which transports Na(+) out of the cell and K(+) into the cell. Inhibits NKA activity in its unphosphorylated state and stimulates activity when phosphorylated. Reduces glutathionylation of the NKA beta-1 subunit ATP1B1, thus reversing glutathionylation-mediated inhibition of ATP1B1. Contributes to female sexual development by maintaining the excitability of neurons which secrete gonadotropin-releasing hormone. {ECO:0000250|UniProtKB:O08589, ECO:0000250|UniProtKB:P56513, ECO:0000250|UniProtKB:Q9Z239}.;
Pathway: cAMP signaling pathway - 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: 0.393
rvis_EVS: 0.52
rvis_percentile_EVS: 80.46

Haploinsufficiency Scores

pHI
hipred: N
hipred_score: 0.462
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.801

Mouse Genome Informatics

Gene name: Fxyd1
Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); muscle phenotype;

Gene ontology

Biological process: potassium ion transport;sodium ion transport;chloride transport;muscle contraction;regulation of heart contraction;negative regulation of protein glutathionylation;regulation of cardiac muscle cell membrane potential;chloride transmembrane transport;positive regulation of sodium ion export across plasma membrane;regulation of sodium ion transmembrane transporter activity
Cellular component: plasma membrane;integral component of plasma membrane;sodium:potassium-exchanging ATPase complex;caveola;intercalated disc;apical plasma membrane;T-tubule;sarcolemma
Molecular function: chloride channel activity;sodium channel regulator activity;ion channel binding;ion channel regulator activity