SLC9A8

solute carrier family 9 member A8, the group of Solute carrier family 9

Basic information

Region (hg38): 20:49812712-49892242

Links

ENSG00000197818 ∙ NCBI:23315 ∙ OMIM:612730 ∙ HGNC:20728 ∙ Uniprot:Q9Y2E8 ∙ 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 SLC9A8 gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC9A8 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		1
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	15	1	0

Variants in SLC9A8

This is a list of pathogenic ClinVar variants found in the SLC9A8 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-49815040-A-G		not specified	Uncertain significance (May 31, 2023)
20-49815094-C-T		not specified	Uncertain significance (Feb 12, 2024)
20-49815114-G-A		not specified	Uncertain significance (Nov 09, 2023)
20-49823077-G-C		not specified	Uncertain significance (Jan 26, 2022)
20-49823105-C-T		not specified	Uncertain significance (Apr 12, 2023)
20-49839562-T-C		not specified	Uncertain significance (Feb 27, 2024)
20-49845087-A-G		not specified	Uncertain significance (Jul 07, 2022)
20-49850837-A-G		not specified	Uncertain significance (Feb 28, 2023)
20-49850842-C-G		not specified	Uncertain significance (Nov 18, 2023)
20-49855438-T-C		not specified	Likely benign (May 26, 2023)
20-49855488-C-T		not specified	Uncertain significance (Dec 15, 2022)
20-49862939-G-A		not specified	Uncertain significance (Feb 14, 2023)
20-49862942-T-A		not specified	Uncertain significance (Jan 11, 2023)
20-49862979-A-G		not specified	Uncertain significance (Jun 05, 2023)
20-49863011-A-G		not specified	Uncertain significance (May 18, 2023)
20-49864739-G-A		not specified	Uncertain significance (Jun 22, 2023)
20-49864767-C-T		not specified	Uncertain significance (Jan 22, 2024)
20-49874725-T-C		not specified	Uncertain significance (Jan 02, 2024)
20-49880936-T-G		not specified	Uncertain significance (Jul 12, 2022)
20-49883909-G-A		not specified	Uncertain significance (Jan 17, 2023)
20-49884040-G-A		not specified	Uncertain significance (Jan 03, 2024)
20-49886878-A-C		not specified	Uncertain significance (Jul 20, 2021)
20-49887840-C-T			Likely benign (Apr 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC9A8	protein_coding	protein_coding	ENST00000417961	16	79530

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.91e-10	0.722	125688	0	59	125747	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.62	266	351	0.757	0.0000201	3927
Missense in Polyphen		71	102.37	0.69359		1109
Synonymous	-0.627	150	141	1.07	0.00000938	1155
Loss of Function	1.50	19	27.5	0.691	0.00000125	340

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000581	0.000574
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000279	0.000272
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000279	0.000272
South Asian	0.000377	0.000359
Other	0.000698	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pH regulation to eliminate acids generated by active metabolism or to counter adverse environmental conditions. Major proton extruding system driven by the inward sodium ion chemical gradient. Plays an important role in signal transduction. {ECO:0000269|PubMed:15522866}.
• Pathway: Sodium/Proton exchangers;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.151

Intolerance Scores

• loftool: 0.811
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.86

Haploinsufficiency Scores

• pHI: 0.0652
• hipred: Y
• hipred_score: 0.541
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.478

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc9a8
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; digestive/alimentary phenotype; vision/eye phenotype; reproductive system phenotype; pigmentation phenotype

Gene ontology

• Biological process: ion transport;sodium ion transmembrane transport;regulation of intracellular pH;potassium ion transmembrane transport;proton transmembrane transport
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: sodium:proton antiporter activity;potassium:proton antiporter activity