SLC35D2

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

Basic information

Region (hg38): 9:96313444-96383711

Links

ENSG00000130958 ∙ NCBI:11046 ∙ OMIM:609182 ∙ HGNC:20799 ∙ Uniprot:Q76EJ3 ∙ 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 SLC35D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC35D2 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						0
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in SLC35D2

This is a list of pathogenic ClinVar variants found in the SLC35D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-96321299-G-C		not specified	Uncertain significance (Jan 03, 2024)
9-96322047-C-T		not specified	Uncertain significance (Nov 25, 2024)
9-96324150-T-G		not specified	Uncertain significance (Jun 04, 2024)
9-96324157-C-T		not specified	Uncertain significance (Dec 19, 2022)
9-96324158-A-G		not specified	Uncertain significance (Aug 05, 2024)
9-96324168-A-G		not specified	Uncertain significance (Apr 24, 2024)
9-96336741-T-C		not specified	Uncertain significance (Dec 27, 2022)
9-96336757-C-T		not specified	Uncertain significance (Oct 27, 2023)
9-96336781-T-C		not specified	Uncertain significance (Jan 03, 2024)
9-96343953-A-G		not specified	Uncertain significance (Jul 05, 2022)
9-96343981-C-T		not specified	Uncertain significance (Dec 06, 2024)
9-96345310-T-C		not specified	Uncertain significance (Jul 11, 2023)
9-96345372-T-G		not specified	Uncertain significance (Feb 11, 2022)
9-96351141-A-C		not specified	Uncertain significance (Oct 22, 2021)
9-96352104-G-A		not specified	Uncertain significance (Apr 25, 2022)
9-96360189-G-T		not specified	Uncertain significance (Dec 28, 2022)
9-96360199-T-C		not specified	Uncertain significance (Dec 20, 2023)
9-96360200-A-T		not specified	Uncertain significance (Jul 19, 2022)
9-96360215-G-C		not specified	Uncertain significance (Mar 25, 2024)
9-96383480-T-C		not specified	Uncertain significance (Aug 31, 2022)
9-96383498-T-C		not specified	Uncertain significance (Jun 07, 2023)
9-96383499-T-C		not specified	Uncertain significance (Nov 30, 2022)
9-96383501-T-C		not specified	Uncertain significance (Dec 22, 2023)
9-96383528-G-T		not specified	Uncertain significance (Apr 25, 2023)
9-96383590-C-A		not specified	Likely benign (Nov 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC35D2	protein_coding	protein_coding	ENST00000253270	12	63005

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.90e-13	0.0163	125696	0	51	125747	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.493	143	161	0.890	0.00000766	2156
Missense in Polyphen		52	62.814	0.82784		793
Synonymous	0.576	58	63.9	0.908	0.00000348	669
Loss of Function	-0.309	18	16.6	1.08	7.03e-7	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000748	0.000745
Ashkenazi Jewish	0.00	0.00
East Asian	0.000769	0.000761
Finnish	0.00	0.00
European (Non-Finnish)	0.000104	0.0000967
Middle Eastern	0.000769	0.000761
South Asian	0.000138	0.000131
Other	0.000168	0.000163

dbNSFP

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}.
• Pathway: Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;HS-GAG biosynthesis;Heparan sulfate/heparin (HS-GAG) metabolism;Glycosaminoglycan metabolism;Metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Galactose metabolism;O-Glycan biosynthesis;Transport of nucleotide sugars (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.824
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.213
• hipred: N
• hipred_score: 0.198
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.391

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc35d2

Gene ontology

• Biological process: glycosaminoglycan biosynthetic process;biological_process;carbohydrate transport;keratan sulfate biosynthetic process;pyrimidine nucleotide-sugar transmembrane transport
• Cellular component: Golgi membrane;cellular_component;Golgi apparatus;integral component of membrane
• 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;antiporter activity;transmembrane transporter activity