FXYD1
Basic information
Region (hg38): 19:35138824-35143109
Previous symbols: [ "PLM" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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.
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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in FXYD1
This is a list of pathogenic ClinVar variants found in the FXYD1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-35140084-C-T | not specified | Uncertain significance (Oct 19, 2024) | ||
| 19-35140135-A-G | not specified | Uncertain significance (Dec 13, 2021) | ||
| 19-35140614-G-C | not specified | Uncertain significance (Mar 29, 2024) | ||
| 19-35141194-C-A | not specified | Uncertain significance (Oct 01, 2024) | ||
| 19-35141199-C-G | not specified | Uncertain significance (Mar 10, 2025) | ||
| 19-35142488-G-A | not specified | Uncertain significance (Mar 22, 2023) |
GnomAD
Source:
| 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:
- 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