SLC9A5

solute carrier family 9 member A5, the group of Solute carrier family 9

Basic information

Region (hg38): 16:67237683-67272191

Links

ENSG00000135740 ∙ NCBI:6553 ∙ OMIM:600477 ∙ HGNC:11078 ∙ Uniprot:Q14940 ∙ 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 SLC9A5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC9A5 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				2		2
missense			41			41
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	2	0

Variants in SLC9A5

This is a list of pathogenic ClinVar variants found in the SLC9A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67237687-G-A		not specified	Likely benign (Jun 02, 2023)
16-67237732-A-C		not specified	Uncertain significance (Nov 13, 2024)
16-67237751-C-G		not specified	Uncertain significance (Dec 27, 2023)
16-67237765-G-C		not specified	Uncertain significance (Dec 16, 2022)
16-67238041-G-A			not provided (-)
16-67238123-C-T		not specified	Uncertain significance (Nov 30, 2022)
16-67238128-G-A		not specified	Uncertain significance (May 08, 2023)
16-67238387-A-T		not specified	Uncertain significance (Mar 31, 2023)
16-67238414-C-T		not specified	Uncertain significance (Oct 26, 2021)
16-67238959-C-T		not specified	Uncertain significance (Sep 25, 2023)
16-67239406-T-C		not specified	Uncertain significance (Mar 31, 2023)
16-67239414-T-C		not specified	Uncertain significance (Oct 26, 2022)
16-67239421-C-T		not specified	Uncertain significance (Apr 12, 2024)
16-67247247-A-G		not specified	Uncertain significance (Nov 20, 2024)
16-67247272-C-A		not specified	Uncertain significance (Dec 12, 2023)
16-67247304-T-C		not specified	Uncertain significance (Sep 13, 2022)
16-67247308-G-C		not specified	Uncertain significance (Feb 22, 2023)
16-67247319-C-T		not specified	Uncertain significance (Dec 03, 2024)
16-67247329-G-T		not specified	Uncertain significance (Dec 20, 2023)
16-67247367-A-G		not specified	Uncertain significance (Feb 07, 2023)
16-67247389-C-A		not specified	Uncertain significance (Jun 21, 2023)
16-67247406-G-T		not specified	Uncertain significance (Aug 21, 2024)
16-67249024-G-T		not specified	Uncertain significance (Aug 10, 2021)
16-67249055-C-T		not specified	Uncertain significance (Oct 12, 2021)
16-67249112-G-A		not specified	Uncertain significance (Jul 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC9A5	protein_coding	protein_coding	ENST00000299798	16	34508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.80e-8	1.00	124802	0	74	124876	0.000296

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.94	341	532	0.641	0.0000319	5743
Missense in Polyphen		107	195.4	0.54759		2154
Synonymous	1.48	192	220	0.873	0.0000131	1893
Loss of Function	3.15	20	42.1	0.476	0.00000249	429

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000628	0.000627
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000278
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000380	0.000379
Middle Eastern	0.000278	0.000278
South Asian	0.00	0.00
Other	0.00116	0.00115

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 (By similarity). {ECO:0000250}.
• Pathway: Beta-agonist/Beta-blocker Pathway, Pharmacodynamics;Sodium/Proton exchangers;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.417
• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.8

Haploinsufficiency Scores

• pHI: 0.324
• hipred: Y
• hipred_score: 0.692
• ghis: 0.642

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.819

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc9a5

Gene ontology

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