SLC9B1

solute carrier family 9 member B1, the group of Solute carrier family 9

Basic information

Region (hg38): 4:102885048-103019719

Previous symbols: [ "NHEDC1" ]

Links

ENSG00000164037 ∙ NCBI:150159 ∙ OMIM:611527 ∙ HGNC:24244 ∙ Uniprot:Q4ZJI4 ∙ 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 SLC9B1 gene.

• Usher syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC9B1 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	2		3
missense			22	7		29
nonsense			1			1
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			8	16	1	25
Total	1	0	32	25	1

Highest pathogenic variant AF is 0.341

Variants in SLC9B1

This is a list of pathogenic ClinVar variants found in the SLC9B1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-102885206-A-G			Likely benign (Jul 25, 2022)
4-102885207-C-A		Wolfram syndrome 2 • CISD2-related disorder	Benign/Likely benign (Dec 12, 2023)
4-102885221-G-C		Wolfram syndrome 2	Pathogenic (Oct 01, 2007)
4-102885221-G-T		Wolfram syndrome 2	Likely pathogenic (Dec 29, 2023)
4-102885230-C-T			Uncertain significance (May 15, 2022)
4-102885232-G-A			Likely benign (Jun 27, 2022)
4-102885254-C-T			Uncertain significance (May 10, 2022)
4-102885256-C-G			Likely benign (Nov 01, 2024)
4-102885256-C-T		CISD2-related disorder	Likely benign (Jan 11, 2023)
4-102885269-T-C		Inborn genetic diseases	Uncertain significance (Mar 25, 2024)
4-102885281-C-T		Wolfram syndrome 2	Uncertain significance (Jan 20, 2024)
4-102885282-G-A		Wolfram syndrome 2	Uncertain significance (May 30, 2024)
4-102885294-C-T		Wolfram syndrome 2	Uncertain significance (Mar 13, 2024)
4-102885295-G-A			Likely benign (Aug 16, 2022)
4-102885316-T-C			Likely benign (May 29, 2022)
4-102885336-T-C			Uncertain significance (Jul 13, 2016)
4-102885338-C-A			Uncertain significance (Feb 23, 2022)
4-102885339-A-T			Uncertain significance (Jul 19, 2022)
4-102885340-A-G			Likely benign (Mar 26, 2022)
4-102885345-A-G		Wolfram syndrome 2	Uncertain significance (Mar 13, 2024)
4-102885347-A-T			Uncertain significance (May 30, 2022)
4-102885351-C-T		Wolfram syndrome 2	Uncertain significance (Aug 01, 2022)
4-102885352-G-A		Wolfram syndrome 2	Benign/Likely benign (Nov 20, 2023)
4-102885372-A-G		Inborn genetic diseases • Wolfram syndrome 2	Uncertain significance (Nov 26, 2024)
4-102885374-A-G		Wolfram syndrome 2	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC9B1	protein_coding	protein_coding	ENST00000296422	11	134692

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.17e-7	0.864	125513	0	217	125730	0.000863

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.874	218	257	0.847	0.0000122	3271
Missense in Polyphen		44	65.753	0.66917		849
Synonymous	1.14	77	90.9	0.847	0.00000442	1022
Loss of Function	1.54	13	20.6	0.632	8.67e-7	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000755	0.000737
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000235	0.000231
European (Non-Finnish)	0.00108	0.00103
Middle Eastern	0.00	0.00
South Asian	0.00242	0.00235
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sperm-specific Na(+)/H(+) exchanger involved in intracellular pH regulation of spermatozoa. Involved in sperm motility and fertility. {ECO:0000250|UniProtKB:Q8C0X2}.
• Pathway: Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.0840

Intolerance Scores

• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.218

Essentials

• essential_gene_CRISPR: 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: Slc9b1

Gene ontology

• Biological process: single fertilization;flagellated sperm motility;ion transmembrane transport;sodium ion transmembrane transport;regulation of intracellular pH;proton transmembrane transport
• Cellular component: plasma membrane;integral component of membrane;sperm principal piece
• Molecular function: sodium:proton antiporter activity