GeneBe

SLC2A9

protein-coding

solute carrier family 2 member 9, the group of Solute carrier family 2

Gene summary

This gene encodes a member of the SLC2A facilitative glucose transporter family. Members of this family play a significant role in maintaining glucose homeostasis. The encoded protein may play a role in the development and survival of chondrocytes in cartilage matrices. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_020041.3

Inheritance

AR, AD, SD

ClinVar variants

P:21U:121B:66

Top phenotype

Hypouricemia, renal, 2

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr4:9,771,153-10,054,936

External References & Databases

Ensembl (ENSG00000109667)NCBI Gene (56606)OMIM (606142)HGNC:13446GenCCUniProt (Q9NRM0)AlphaFoldClinVar (SLC2A9)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~283.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hereditary renal hypouricemiaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009071

Submitter: Orphanet

hypouricemia, renal, 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012793

Submitter: Labcorp Genetics (formerly Invitae)

hypouricemia, renal, 2LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0012793

Submitter: Labcorp Genetics (formerly Invitae)

hypouricemia, renal, 2MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0012793

Submitter: Ambry Genetics

hypouricemia, renal, 2STRONG

Inheritance Pattern: SD

Disease ID:MONDO:0012793

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Hypouricemia, renal, 2AD/AR

Manifestation: Renal

Intervention: Renal

Rationale: The condition may be associated with complications including exercise-induced acute renal failure and nephrolithiasis, and preventive measures (eg, related to exercise) may be beneficial

Comments: The youngest reported individual was an adult, but morbidity could theoretically appear earlier

Refs: 9026395; 19926891; 22132964; 21536615Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC2A9 variants in ClinVar

7 Conditions Cataloged
not providedTotal: 155
Hypouricemia, renal, 2Total: 85
Inborn genetic diseasesTotal: 54
SLC2A9-related disorderTotal: 15
not specifiedTotal: 4
Renal tubulopathiesTotal: 1
SchizophreniaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020041.3. 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.

EffectPLPVUSLBBSum
synonymous
7
clinvar
49
clinvar
6
clinvar
 62
missense
2
clinvar
7
clinvar
109
clinvar
8
clinvar
3
clinvar
 129
nonsense
1
clinvar
1
clinvar
 2
start loss
0
frameshift
2
clinvar
3
clinvar
 5
splice donor/acceptor (+/-2bp)
1
clinvar
5
clinvar
4
clinvar
 10
Total615121579208

Highest pathogenic variant AF is 0.00027320578

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_020041.3RefSeqNP_064425.212MANE Select
ENST00000264784.8EnsemblENSP00000264784.312MANE Select
NM_001001290.2RefSeqNP_001001290.112Standard
ENST00000309065.7EnsemblENSP00000311383.312Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Uricosurics Pathway, Pharmacodynamics
  • Nuclear Receptors Meta-Pathway
  • NRF2 pathway
  • SLC-mediated transmembrane transport
  • Transport of small molecules

Biological Process

  • hexose transmembrane transport
  • urate transport
  • urate metabolic process
  • proton transmembrane transport
  • glucose transmembrane transport

Molecular Function

  • carbohydrate:proton symporter activity
  • glucose transmembrane transporter activity
  • urate transmembrane transporter activity
  • transmembrane transporter activity

Cellular Component

  • plasma membrane
  • integral component of membrane
  • basolateral plasma membrane
  • apical plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000264784
Coding exons
12
Length
283784
Individuals with no LoFs
125700
Homozygous LoFs
0
Heterozygous LoFs
48
Defined
125748
p
0.000191
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.1243052991.020.00001703457
Missense (PolyPhen)114124.540.915381538
Synonymous-1.901571291.210.000008061148
Loss of Function1.051722.40.7619.67e-7265

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000310.00031rare
Latino/Admixed American0.000320.00032rare
Ashkenazi Jewish00.0absent
East Asian0.000600.00060rare
Finnish00.0absent
European (Non-Finnish)0.000130.00013rare
South Asian0.000200.00020rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Transport urate and fructose. May have a role in the urate reabsorption by proximal tubules. Also transports glucose at low rate. {ECO:0000269|PubMed:14739288, ECO:0000269|PubMed:18327257}.;
Disease
DISEASE: Hypouricemia renal 2 (RHUC2) [MIM:612076]: A disorder characterized by impaired uric acid reabsorption at the apical membrane of proximal renal tubule cells, and high urinary urate excretion. Patients often appear asymptomatic, but may be subject to exercise-induced acute renal failure, chronic renal dysfunction and nephrolithiasis. {ECO:0000269|PubMed:19026395, ECO:0000269|PubMed:19926891, ECO:0000269|PubMed:21810765}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Intolerance Scores

LoFtool
0.433
RVIS EVS
1.23
RVIS percentile EVS
93.25

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.340

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh
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