GeneBe

SLC35D2

protein-coding

solute carrier family 35 member D2, the group of Solute carrier family 35

Gene summary

Nucleotide sugars, which are synthesized in the cytosol or the nucleus, are high-energy donor substrates for glycosyltransferases located in the lumen of the endoplasmic reticulum and Golgi apparatus. Translocation of nucleotide sugars from the cytosol into the lumen compartment is mediated by specific nucleotide sugar transporters, such as SLC35D2 (Suda et al., 2004 [PubMed 15082721]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_007001.3

Inheritance

—

ClinVar variants

U:52B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.08

Max pathogenic AF

—

Genomic locus

chr9:96,313,444-96,383,711

External References & Databases

Ensembl (ENSG00000130958)NCBI Gene (11046)OMIM (609182)HGNC:20799GenCCUniProt (Q76EJ3)AlphaFoldClinVar (SLC35D2)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~70.3 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 SLC35D2 variants in ClinVar

1 Conditions Cataloged
not specifiedTotal: 50

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007001.3. 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
1
clinvar
 1
missense
49
clinvar
1
clinvar
 50
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
2
clinvar
 2
Total00521053
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_007001.3RefSeqNP_008932.212MANE Select
ENST00000253270.13EnsemblENSP00000253270.712MANE Select
NM_001286990.2RefSeqNP_001273919.19Standard
ENST00000375257.2EnsemblENSP00000364406.16Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Metabolism of carbohydrates
  • Keratan sulfate biosynthesis
  • Keratan sulfate/keratin metabolism
  • HS-GAG biosynthesis
  • Heparan sulfate/heparin (HS-GAG) metabolism

Biological Process

  • glycosaminoglycan biosynthetic process
  • biological_process
  • carbohydrate transport
  • keratan sulfate biosynthetic process
  • pyrimidine nucleotide-sugar transmembrane transport

Molecular Function

  • nucleotide-sugar transmembrane transporter activity
  • UDP-glucuronic acid transmembrane transporter activity
  • UDP-N-acetylglucosamine transmembrane transporter activity
  • UDP-N-acetylgalactosamine transmembrane transporter activity
  • pyrimidine nucleotide-sugar transmembrane transporter activity

Cellular Component

  • Golgi membrane
  • cellular_component
  • Golgi apparatus
  • integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000253270
Coding exons
12
Length
63005
Individuals with no LoFs
125696
Homozygous LoFs
0
Heterozygous LoFs
51
Defined
125747
p
0.000203
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4931431610.8900.000007662156
Missense (PolyPhen)5262.8140.82784793
Synonymous0.5765863.90.9080.00000348669
Loss of Function-0.3091816.61.087.03e-7224

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.000500.00049rare
Ashkenazi Jewish00.0absent
East Asian0.000770.00076rare
Finnish00.0absent
European (Non-Finnish)0.000100.000097rare
South Asian0.000140.00013rare
Other0.000170.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Antiporter transporting nucleotide sugars such as UDP-N- acetylglucosamine (UDP-GlcNAc), UDP-glucose (UDP-Glc) and GDP- mannose (GDP-Man) pooled in the cytosol into the lumen of the Golgi in exchange for the corresponding nucleosides monophosphates (UMP for UDP-sugars and GMP for GDP-sugars). May take part in heparan sulfate synthesis by supplying UDP-Glc-NAc, the donor substrate, and thus be involved in growth factor signaling. {ECO:0000269|PubMed:15082721, ECO:0000269|PubMed:15607426}.;

Recessive Scores

pRec
0.122

Intolerance Scores

LoFtool
0.824
RVIS EVS
-0.27
RVIS percentile EVS
34.32

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.391

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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