SLC9A2

solute carrier family 9 member A2, the group of Solute carrier family 9

Basic information

Region (hg38): 2:102619553-102711355

Previous symbols: [ "NHE2" ]

Links

ENSG00000115616 ∙ NCBI:6549 ∙ OMIM:600530 ∙ HGNC:11072 ∙ Uniprot:Q9UBY0 ∙ 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 SLC9A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC9A2 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in SLC9A2

This is a list of pathogenic ClinVar variants found in the SLC9A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-102619930-C-T		not specified	Uncertain significance (Nov 22, 2023)
2-102619954-T-A		not specified	Uncertain significance (Oct 19, 2024)
2-102619963-G-A		not specified	Uncertain significance (Jan 29, 2024)
2-102620009-G-C		not specified	Uncertain significance (Dec 04, 2024)
2-102620011-G-C		not specified	Uncertain significance (Dec 22, 2023)
2-102620024-G-A		not specified	Uncertain significance (Mar 19, 2024)
2-102635468-G-A		Ascending aortic dissection	association (Feb 01, 2021)
2-102657621-T-C		not specified	Uncertain significance (Apr 25, 2022)
2-102657734-G-A		not specified	Uncertain significance (Sep 22, 2022)
2-102657875-G-A		not specified	Uncertain significance (Nov 09, 2021)
2-102665157-G-A		not specified	Uncertain significance (May 14, 2024)
2-102665172-G-A		not specified	Uncertain significance (Apr 12, 2023)
2-102665253-A-G		not specified	Uncertain significance (Mar 15, 2024)
2-102665313-A-G		not specified	Uncertain significance (Nov 27, 2023)
2-102665317-C-T		not specified	Uncertain significance (Jan 30, 2024)
2-102683266-C-G		not specified	Uncertain significance (Jun 25, 2024)
2-102683407-G-A		not specified	Uncertain significance (Aug 28, 2024)
2-102683436-G-A		not specified	Uncertain significance (Dec 22, 2023)
2-102683446-C-A		not specified	Uncertain significance (Jun 16, 2023)
2-102684268-G-A		not specified	Uncertain significance (Oct 08, 2024)
2-102684278-G-A		not specified	Uncertain significance (Jun 10, 2024)
2-102694459-T-C		not specified	Uncertain significance (Dec 15, 2023)
2-102694477-G-A		not specified	Uncertain significance (Oct 12, 2021)
2-102701144-C-T		not specified	Uncertain significance (Sep 24, 2024)
2-102701173-G-A		not specified	Uncertain significance (Jul 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC9A2	protein_coding	protein_coding	ENST00000233969	12	91612

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00242	0.998	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	331	458	0.722	0.0000253	5291
Missense in Polyphen		144	219.66	0.65556		2514
Synonymous	-0.431	192	185	1.04	0.0000108	1642
Loss of Function	3.94	12	38.4	0.313	0.00000256	388

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000668	0.000668
Ashkenazi Jewish	0.000301	0.000298
East Asian	0.000109	0.000109
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.0000657	0.0000653
Other	0.000326	0.000326

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. Seems to play an important role in colonic sodium absorption.
• 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: 0.189

Intolerance Scores

• loftool: 0.594
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.01

Haploinsufficiency Scores

• pHI: 0.549
• hipred: Y
• hipred_score: 0.630
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.814

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc9a2
• Phenotype: immune system phenotype; digestive/alimentary phenotype; reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: ion transport;protein localization;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