SLC35C2

solute carrier family 35 member C2, the group of Solute carrier family 35

Basic information

Region (hg38): 20:46345980-46364458

Previous symbols: [ "C20orf5", "OVCOV1" ]

Links

ENSG00000080189NCBI:51006OMIM:619530HGNC:17117Uniprot:Q9NQQ7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC35C2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC35C2 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
clinvar
1
missense
30
clinvar
1
clinvar
31
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 30 2 0

Variants in SLC35C2

This is a list of pathogenic ClinVar variants found in the SLC35C2 region.

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

Position Type Phenotype Significance ClinVar
20-46350435-T-C not specified Uncertain significance (Jan 02, 2024)3164348
20-46350449-C-T not specified Likely benign (Sep 30, 2024)3444076
20-46350456-T-G not specified Uncertain significance (Jan 23, 2023)2478211
20-46350788-C-T not specified Uncertain significance (Oct 07, 2024)3444080
20-46350791-G-A not specified Uncertain significance (Nov 13, 2024)3444079
20-46350811-C-A not specified Uncertain significance (Jan 08, 2024)3164353
20-46350819-G-A Likely benign (Nov 01, 2022)2652368
20-46350830-A-T not specified Uncertain significance (Jun 13, 2023)2559972
20-46350851-C-T not specified Uncertain significance (Sep 04, 2024)3444085
20-46350857-G-C not specified Uncertain significance (Feb 22, 2023)2486959
20-46352190-A-C not specified Uncertain significance (Jun 11, 2024)3319579
20-46352193-C-T not specified Uncertain significance (Dec 14, 2023)2360781
20-46352200-T-C not specified Uncertain significance (Jan 05, 2022)2401992
20-46352202-T-A not specified Uncertain significance (Sep 10, 2024)3444086
20-46354948-C-T not specified Uncertain significance (Mar 26, 2024)3319578
20-46354950-A-G not specified Uncertain significance (Feb 22, 2023)2487819
20-46354959-T-C not specified Uncertain significance (Feb 13, 2024)3164352
20-46355097-T-G not specified Uncertain significance (Dec 18, 2023)3164351
20-46355205-C-G not specified Uncertain significance (Sep 27, 2024)3444077
20-46355226-G-C not specified Uncertain significance (Sep 14, 2022)2311827
20-46355237-G-A not specified Uncertain significance (Sep 24, 2024)3444078
20-46355821-A-G not specified Uncertain significance (Nov 17, 2022)3164350
20-46356625-G-A not specified Uncertain significance (Nov 13, 2024)3444075
20-46357647-A-G not specified Uncertain significance (Dec 19, 2023)3164349
20-46357665-C-A not specified Uncertain significance (Sep 03, 2024)3444084

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC35C2protein_codingprotein_codingENST00000372227 914877
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001470.9701256850631257480.000251
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.231692200.7670.00001322351
Missense in Polyphen3356.3890.58522644
Synonymous-0.8371131021.110.00000663780
Loss of Function1.92715.10.4656.40e-7175

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003630.000362
Ashkenazi Jewish0.000.00
East Asian0.0005740.000544
Finnish0.000.00
European (Non-Finnish)0.0003260.000325
Middle Eastern0.0005740.000544
South Asian0.0001990.000196
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: May play an important role in the cellular response to tissue hypoxia. May be either a GDP-fucose transporter that competes with SLC35C1 for GDP-fucose, or a factor that otherwise enhances the fucosylation of Notch and is required for optimal Notch signaling in mammalian cells. {ECO:0000269|PubMed:20837470}.;

Recessive Scores

pRec
0.0986

Intolerance Scores

loftool
0.242
rvis_EVS
-0.62
rvis_percentile_EVS
17.16

Haploinsufficiency Scores

pHI
0.118
hipred
N
hipred_score
0.390
ghis
0.557

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.508

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Slc35c2
Phenotype

Gene ontology

Biological process
negative regulation of gene expression;UDP-glucose transmembrane transport;protein O-linked fucosylation;positive regulation of Notch signaling pathway
Cellular component
nucleoplasm;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cis-Golgi network;integral component of membrane;endoplasmic reticulum-Golgi intermediate compartment membrane
Molecular function
antiporter activity;transmembrane transporter activity