FXYD6-FXYD2

FXYD6-FXYD2 readthrough

Basic information

Region (hg38): 11:117820162-117876667

Links

ENSG00000255245 ∙ NCBI:100533181 ∙ ∙ HGNC:39978 ∙ ∙ ∙ 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-FXYD2 gene.

• not provided (58 variants)
• Renal hypomagnesemia 2 (26 variants)
• Inborn genetic diseases (4 variants)
• not specified (2 variants)
• Renal Hypomagnesemia, Dominant (2 variants)
• FXYD2-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FXYD6-FXYD2 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			1	9	2	12
missense	1		6	4	2	13
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			5	3	2	10
splice region						0
non coding			1	9	15	25
Total	1	0	14	25	21

Variants in FXYD6-FXYD2

This is a list of pathogenic ClinVar variants found in the FXYD6-FXYD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-117820164-C-T		Renal hypomagnesemia 2	Benign (Jan 12, 2018)
11-117820191-G-A		Renal Hypomagnesemia, Dominant	Uncertain significance (Jun 14, 2016)
11-117820203-A-C		Renal hypomagnesemia 2	Benign (Jan 13, 2018)
11-117820230-T-C		Renal hypomagnesemia 2	Uncertain significance (Jan 13, 2018)
11-117820255-A-T		Renal hypomagnesemia 2	Uncertain significance (Jan 13, 2018)
11-117820274-G-A		Renal hypomagnesemia 2	Benign (Jan 12, 2018)
11-117820301-G-T		Renal hypomagnesemia 2	Benign (Jan 13, 2018)
11-117820308-C-T		Renal hypomagnesemia 2	Benign (Jan 13, 2018)
11-117820430-C-T			Benign (Nov 11, 2018)
11-117820433-C-T			Benign (Nov 11, 2018)
11-117820548-C-A			Likely benign (Nov 08, 2020)
11-117820637-C-T			Benign (May 24, 2021)
11-117820660-G-T		Renal hypomagnesemia 2 • not specified	Benign/Likely benign (Nov 22, 2019)
11-117820665-C-G		FXYD2-related disorder	Likely benign (Aug 24, 2020)
11-117820666-C-A		FXYD2-related disorder	Likely benign (Dec 20, 2022)
11-117820671-G-A		Renal hypomagnesemia 2	Benign (Nov 26, 2019)
11-117820675-C-A		Renal hypomagnesemia 2	Benign/Likely benign (Oct 10, 2022)
11-117820675-C-T		Renal hypomagnesemia 2	Likely benign (Mar 18, 2022)
11-117820678-C-T		Renal hypomagnesemia 2	Benign (Jan 16, 2024)
11-117820681-A-G		FXYD6-FXYD2-related disorder	Likely benign (Aug 09, 2022)
11-117820686-C-T			Uncertain significance (Jun 26, 2023)
11-117820688-T-C		not specified	Uncertain significance (Dec 20, 2023)
11-117820690-G-A		Renal hypomagnesemia 2	Benign/Likely benign (May 12, 2023)
11-117820702-G-A			Likely benign (Nov 10, 2023)
11-117820702-G-T			Likely benign (Nov 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FXYD6-FXYD2	protein_coding	protein_coding	ENST00000532984	7	56505

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.850	0.149	125704	0	1	125705	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.270	54	59.9	0.902	0.00000316	699
Missense in Polyphen		6	18.21	0.32949		235
Synonymous	-0.0125	25	24.9	1.00	0.00000149	217
Loss of Function	2.73	1	10.6	0.0942	4.52e-7	117

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.189
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

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

Gene ontology

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