FXYD7

FXYD domain containing ion transport regulator 7

Basic information

Region (hg38): 19:35143250-35154302

Links

ENSG00000221946 ∙ NCBI:53822 ∙ OMIM:606684 ∙ HGNC:4034 ∙ Uniprot:P58549 ∙ 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 FXYD7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FXYD7 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in FXYD7

This is a list of pathogenic ClinVar variants found in the FXYD7 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35151257-A-G		not specified	Uncertain significance (May 27, 2022)
19-35151300-G-T		not specified	Uncertain significance (Nov 14, 2024)
19-35151667-T-C		not specified	Uncertain significance (Sep 03, 2024)
19-35153903-G-A		not specified	Uncertain significance (Jan 09, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FXYD7	protein_coding	protein_coding	ENST00000270310	6	11051

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00519	0.720	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.935	26	43.3	0.600	0.00000219	509
Missense in Polyphen		7	17.147	0.40823		206
Synonymous	-0.507	20	17.3	1.16	0.00000104	157
Loss of Function	0.757	4	6.00	0.667	2.56e-7	77

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)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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: 0.113

Intolerance Scores

• loftool: 0.718
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.506
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.189

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fxyd7

Gene ontology

• Biological process: ion transport;regulation of sodium ion transmembrane transporter activity
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding;sodium channel regulator activity;ATPase binding;ion channel regulator activity