FXYD6

FXYD domain containing ion transport regulator 6

Basic information

Region (hg38): 11:117836976-117877486

Links

ENSG00000137726

∙ NCBI:53826 ∙ OMIM:606683 ∙ HGNC:4030 ∙ Uniprot:Q9H0Q3 ∙ 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 FXYD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FXYD6 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			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in FXYD6

This is a list of pathogenic ClinVar variants found in the FXYD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-117840321-T-C		not specified	Uncertain significance (Mar 07, 2024)	3097577
11-117840325-C-T		not specified	Uncertain significance (Jan 18, 2023)	2464690

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FXYD6	protein_coding	protein_coding	ENST00000526014	6	40509

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.619	0.374	125673	0	1	125674	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.778	36	51.7	0.696	0.00000277	613
Missense in Polyphen		10	19.292	0.51835		207
Synonymous	-0.603	23	19.6	1.17	0.00000109	172
Loss of Function	2.16	1	7.31	0.137	3.09e-7	87

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)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Pathway: Ion channel transport;Ion homeostasis;Transport of small molecules;Cardiac conduction;Muscle contraction;Ion transport by P-type ATPases (Consensus)

Recessive Scores

pRec: 0.130

Intolerance Scores

loftool: 0.310
rvis_EVS: 0.24
rvis_percentile_EVS: 68.72

Haploinsufficiency Scores

pHI: 0.313
hipred: N
hipred_score: 0.189
ghis: 0.582

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

Gene name: Fxyd6
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Zebrafish Information Network

Gene name: fxyd6
Affected structure: ceratohyal cartilage
Phenotype tag: abnormal
Phenotype quality: deformed

Gene ontology

Biological process: ion transport;biological_process;regulation of sodium ion transmembrane transporter activity
Cellular component: plasma membrane;glutamatergic synapse;integral component of postsynaptic membrane;integral component of presynaptic membrane
Molecular function: molecular_function;protein binding;sodium channel regulator activity;ion channel regulator activity