SLC9B2

solute carrier family 9 member B2, the group of Solute carrier family 9

Basic information

Region (hg38): 4:103019868-103085829

Previous symbols: [ "NHEDC2" ]

Links

ENSG00000164038 ∙ NCBI:133308 ∙ OMIM:611789 ∙ HGNC:25143 ∙ Uniprot:Q86UD5 ∙ 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 SLC9B2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC9B2 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			26		1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	3

Variants in SLC9B2

This is a list of pathogenic ClinVar variants found in the SLC9B2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-103026390-C-T		not specified	Uncertain significance (May 30, 2024)
4-103026546-C-T		not specified	Uncertain significance (Aug 04, 2023)
4-103026566-T-C		not specified	Uncertain significance (Jun 22, 2024)
4-103028755-T-C		not specified	Uncertain significance (Apr 01, 2022)
4-103028789-C-A		not specified	Uncertain significance (Aug 02, 2021)
4-103028809-C-T		not specified	Uncertain significance (Apr 01, 2024)
4-103028859-A-G		not specified	Uncertain significance (Aug 08, 2023)
4-103028866-C-T		not specified	Uncertain significance (Jul 25, 2023)
4-103031712-G-C			Benign (Jan 30, 2018)
4-103043305-G-T			Benign (Aug 08, 2017)
4-103043316-T-C		not specified	Uncertain significance (Dec 30, 2023)
4-103043360-C-T		not specified	Uncertain significance (Dec 09, 2023)
4-103044897-C-T		not specified	Uncertain significance (Jul 06, 2021)
4-103044907-A-G		not specified	Uncertain significance (Apr 25, 2023)
4-103044931-C-T		not specified	Uncertain significance (Mar 24, 2023)
4-103044975-A-G		not specified	Uncertain significance (Jan 05, 2022)
4-103044981-T-C		not specified	Uncertain significance (Feb 22, 2023)
4-103044991-T-C		not specified	Uncertain significance (Jan 23, 2024)
4-103047090-T-A		not specified	Uncertain significance (Dec 16, 2022)
4-103047090-T-G		not specified	Uncertain significance (Oct 20, 2023)
4-103047139-G-A			Benign (Jan 30, 2018)
4-103047158-T-A		not specified	Uncertain significance (May 20, 2024)
4-103048953-G-A		not specified	Uncertain significance (Jan 31, 2024)
4-103048974-G-C		not specified	Uncertain significance (Jan 04, 2024)
4-103048978-C-G		not specified	Uncertain significance (Mar 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC9B2	protein_coding	protein_coding	ENST00000394785	11	65962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000758	0.981	125688	0	60	125748	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0531	284	281	1.01	0.0000131	3446
Missense in Polyphen		109	94.316	1.1557		1191
Synonymous	0.876	91	102	0.890	0.00000518	1124
Loss of Function	2.12	12	23.0	0.522	0.00000107	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000956	0.000950
Ashkenazi Jewish	0.00	0.00
East Asian	0.000391	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000197	0.000193
Middle Eastern	0.000391	0.000381
South Asian	0.000132	0.000131
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Na(+)/H(+) antiporter that extrudes Na(+) or Li(+) in exchange for external protons across the membrane (PubMed:18000046, PubMed:28154142, PubMed:22948142, PubMed:18508966). Contributes to the regulation of intracellular pH, sodium homeostasis, and cell volume. Plays an important role for insulin secretion and clathrin-mediated endocytosis in beta- cells (By similarity). Involved in sperm motility and fertility (By similarity). It is controversial whether SLC9B2 plays a role in osteoclast differentiation or not (By similarity). {ECO:0000250|UniProtKB:Q5BKR2, ECO:0000269|PubMed:18000046, ECO:0000269|PubMed:18508966, ECO:0000269|PubMed:22948142, ECO:0000269|PubMed:28154142}.
• Pathway: Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.25

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.376
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc9b2
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: sodium ion transport;flagellated sperm motility;ion transmembrane transport;sodium ion transmembrane transport;regulation of insulin secretion involved in cellular response to glucose stimulus;clathrin-dependent endocytosis;proton transmembrane transport;positive regulation of osteoclast development
• Cellular component: mitochondrial inner membrane;plasma membrane;endosome membrane;integral component of membrane;basolateral plasma membrane;apical plasma membrane;cell junction;synaptic vesicle membrane;mitochondrial membrane;sperm principal piece
• Molecular function: monovalent cation:proton antiporter activity;lithium:proton antiporter activity;sodium:proton antiporter activity;identical protein binding