SLC9B1

protein-coding

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

Gene summary

The protein encoded by this gene is a sodium/hydrogen exchanger and transmembrane protein. Highly conserved orthologs of this gene have been found in other mammalian species. The expression of this gene may be limited to testis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

Previous symbols:

NHEDC1

MANE transcript

NM_139173.4

Inheritance

—

ClinVar variants

U:57B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr4:102,885,048-103,019,719

External References & Databases

Ensembl (ENSG00000164037)

Transcript & Mutation Effects

hg38 • Region Span ~134.7 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC9B1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_139173.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			54 clinvar	6 clinvar		60
nonsense			1 clinvar	1 clinvar		2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	57	9	0	66

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 141 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_139173.4	RefSeq	NP_631912.3	11	MANE Select
ENST00000296422.12	Ensembl	ENSP00000296422.7	11	MANE Select
NM_001100874.3	RefSeq	NP_001094344.2	11	Standard
ENST00000394789.7	Ensembl	ENSP00000378269.3	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Stimuli-sensing channels
Ion channel transport
Transport of small molecules

Biological Process

single fertilization
flagellated sperm motility
ion transmembrane transport
sodium ion transmembrane transport
regulation of intracellular pH

Molecular Function

sodium:proton antiporter activity

Cellular Component

plasma membrane
integral component of membrane
sperm principal piece

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296422
Coding exons: 11
Length: 134692
Individuals with no LoFs: 125513
Homozygous LoFs: 0
Heterozygous LoFs: 217
Defined: 125730
p: 0.000863

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.874	218	257	0.847	0.0000122	3271
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00018	rare
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.0011	0.0010	notable
South Asian	0.0024	0.0024	notable
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0840

Intolerance Scores

RVIS EVS: 0.26
RVIS percentile EVS: 70.44

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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