FXYD3

FXYD domain containing ion transport regulator 3, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 19:35115823-35124324

Previous symbols: [ "PLML" ]

Links

ENSG00000089356 ∙ NCBI:5349 ∙ OMIM:604996 ∙ HGNC:4027 ∙ Uniprot:Q14802 ∙ 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 FXYD3 gene.

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.

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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	4		8
Total	0	0	11	5	0

Variants in FXYD3

This is a list of pathogenic ClinVar variants found in the FXYD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35117342-G-C		not specified	Uncertain significance (Oct 18, 2021)
19-35119171-C-T		not specified	Likely benign (Jul 05, 2023)
19-35119225-A-C		not specified	Uncertain significance (Nov 23, 2022)
19-35119228-G-A		not specified	Uncertain significance (Feb 07, 2023)
19-35119242-C-T		not specified	Likely benign (Dec 18, 2023)
19-35119249-C-T		not specified	Likely benign (Jul 17, 2023)
19-35119369-G-T		not specified	Likely benign (Apr 07, 2022)
19-35119372-C-T		not specified	Uncertain significance (Aug 13, 2021)
19-35121081-T-C		not specified	Uncertain significance (Oct 10, 2023)
19-35121095-G-A		not specified	Uncertain significance (May 31, 2023)
19-35121231-G-T		not specified	Uncertain significance (Dec 13, 2022)
19-35122782-G-T		not specified	Uncertain significance (May 24, 2023)
19-35122806-G-A		not specified	Likely benign (Feb 27, 2023)
19-35122944-C-A		not specified	Uncertain significance (Sep 08, 2024)
19-35123275-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-35123305-C-A		not specified	Uncertain significance (Oct 07, 2024)

GnomAD

Source: gnomAD

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: 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 (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

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

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