FXYD3
Basic information
Region (hg38): 19:35115823-35124324
Previous symbols: [ "PLML" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (23 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FXYD3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005971.4. 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 | 12 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 12 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FXYD3 | protein_coding | protein_coding | ENST00000604255 | 9 | 8497 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000101 | 0.577 | 125737 | 0 | 10 | 125747 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0863 | 78 | 80.2 | 0.973 | 0.00000433 | 920 |
| Missense in Polyphen | 21 | 19.637 | 1.0694 | 241 | ||
| Synonymous | -0.761 | 36 | 30.6 | 1.17 | 0.00000192 | 271 |
| Loss of Function | 0.791 | 9 | 11.9 | 0.753 | 5.93e-7 | 135 |
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) | 0.0000806 | 0.0000791 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000174 | 0.000163 |
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 (PubMed:17077088). Reduces glutathionylation of the NKA beta-1 subunit ATP1B1, thus reversing glutathionylation-mediated inhibition of ATP1B1 (PubMed:21454534). Induces a hyperpolarization-activated chloride current when expressed in Xenopus oocytes (PubMed:7836447). {ECO:0000269|PubMed:17077088, ECO:0000269|PubMed:21454534, ECO:0000269|PubMed:7836447}.; FUNCTION: Isoform 2: Decreases the apparent K+ affinity of the sodium/potassium-transporting ATPase only at slightly negative and positive membrane potentials and increases the apparent Na+ affinity over a large range of membrane potentials. {ECO:0000269|PubMed:17077088}.;
- Pathway
- Ion channel transport;Ion homeostasis;Transport of small molecules;Cardiac conduction;Muscle contraction;Ion transport by P-type ATPases
(Consensus)
Recessive Scores
- pRec
- 0.0950
Intolerance Scores
- loftool
- 0.578
- rvis_EVS
- 0.73
- rvis_percentile_EVS
- 86.08
Haploinsufficiency Scores
- pHI
- 0.123
- hipred
- N
- hipred_score
- 0.112
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.961
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fxyd3
- Phenotype
Gene ontology
- Biological process
- potassium ion transport;sodium ion transport;chloride transport;chloride transmembrane transport;regulation of sodium ion transmembrane transporter activity
- Cellular component
- plasma membrane;integral component of plasma membrane;extracellular exosome
- Molecular function
- chloride channel activity;sodium channel regulator activity;ion channel regulator activity