FXYD5

FXYD domain containing ion transport regulator 5

Basic information

Region (hg38): 19:35154729-35169881

Links

ENSG00000089327 ∙ NCBI:53827 ∙ OMIM:606669 ∙ HGNC:4029 ∙ Uniprot:Q96DB9 ∙ 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 FXYD5 gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FXYD5 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	2		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in FXYD5

This is a list of pathogenic ClinVar variants found in the FXYD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35155555-C-T		not specified	Uncertain significance (Jul 19, 2022)
19-35155566-C-A		not specified	Uncertain significance (Mar 07, 2024)
19-35155566-C-T		not specified	Uncertain significance (Dec 22, 2023)
19-35155567-G-A		not specified	Uncertain significance (Sep 27, 2021)
19-35155575-C-G		not specified	Uncertain significance (May 31, 2023)
19-35157427-C-T		not specified	Uncertain significance (Jun 11, 2021)
19-35157493-G-A		not specified	Likely benign (Jan 26, 2022)
19-35160789-A-G			Uncertain significance (-)
19-35164173-A-C		not specified	Uncertain significance (May 26, 2023)
19-35164201-C-T		not specified	Uncertain significance (Nov 28, 2023)
19-35164224-C-T		not specified	Uncertain significance (Apr 07, 2022)
19-35166256-C-T		not specified	Uncertain significance (Feb 10, 2022)
19-35166265-C-T		not specified	Uncertain significance (Dec 16, 2022)
19-35169590-G-A		not specified	Likely benign (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FXYD5	protein_coding	protein_coding	ENST00000342879	8	15154

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00209	0.922	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.170	101	106	0.954	0.00000597	1129
Missense in Polyphen		30	34.213	0.87685		342
Synonymous	-0.209	45	43.3	1.04	0.00000252	371
Loss of Function	1.55	6	11.7	0.512	5.96e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000940	0.0000940
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in down-regulation of E-cadherin which results in reduced cell adhesion. Promotes metastasis. {ECO:0000269|PubMed:11756660}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.640
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.44

Haploinsufficiency Scores

• pHI: 0.0618
• hipred: N
• hipred_score: 0.273
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0794

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Fxyd5

Gene ontology

• Biological process: ion transport;microvillus assembly;negative regulation of calcium-dependent cell-cell adhesion;regulation of sodium ion transmembrane transporter activity
• Cellular component: integral component of membrane
• Molecular function: actin binding;protein binding;sodium channel regulator activity;cadherin binding;ion channel regulator activity