SLC35B3

solute carrier family 35 member B3, the group of Solute carrier family 35

Basic information

Region (hg38): 6:8411435-8435561

Previous symbols: [ "C6orf196" ]

Links

ENSG00000124786 ∙ NCBI:51000 ∙ OMIM:610845 ∙ HGNC:21601 ∙ Uniprot:Q9H1N7 ∙ 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 SLC35B3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC35B3 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			17	2		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	17	2	0

Variants in SLC35B3

This is a list of pathogenic ClinVar variants found in the SLC35B3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-8413584-C-T		not specified	Uncertain significance (Mar 01, 2023)
6-8413589-A-G		not specified	Uncertain significance (Oct 29, 2021)
6-8413616-G-A		not specified	Uncertain significance (Sep 22, 2022)
6-8413681-C-A		not specified	Likely benign (Mar 29, 2024)
6-8413686-C-G		not specified	Uncertain significance (Jan 26, 2022)
6-8413698-A-G		not specified	Uncertain significance (Nov 27, 2024)
6-8414920-G-A		not specified	Uncertain significance (Dec 23, 2022)
6-8416904-C-T		not specified	Uncertain significance (Mar 19, 2024)
6-8416970-G-A		not specified	Uncertain significance (Nov 15, 2024)
6-8417404-T-C		not specified	Uncertain significance (Jun 29, 2022)
6-8417461-T-G		not specified	Uncertain significance (Nov 14, 2024)
6-8417484-G-A		not specified	Uncertain significance (May 09, 2023)
6-8419609-T-C		not specified	Uncertain significance (Nov 13, 2023)
6-8419639-C-T		not specified	Uncertain significance (Nov 30, 2022)
6-8419662-G-A		not specified	Uncertain significance (Jun 28, 2022)
6-8419675-C-T		not specified	Uncertain significance (Oct 09, 2024)
6-8420753-T-G		not specified	Uncertain significance (Jan 09, 2024)
6-8420787-T-C		not specified	Uncertain significance (May 01, 2022)
6-8420793-T-C		not specified	Likely benign (Apr 25, 2022)
6-8420808-C-A		not specified	Uncertain significance (Aug 19, 2024)
6-8428013-G-A		not specified	Uncertain significance (Aug 15, 2023)
6-8428033-A-G		not specified	Uncertain significance (Aug 02, 2021)
6-8428043-C-A		not specified	Uncertain significance (Oct 06, 2023)
6-8429922-T-C		not specified	Uncertain significance (Aug 09, 2021)
6-8429929-G-A		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC35B3	protein_coding	protein_coding	ENST00000379660	10	22494

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.36e-10	0.104	125666	0	81	125747	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.501	184	204	0.901	0.00000990	2594
Missense in Polyphen		60	69.595	0.86213		909
Synonymous	1.29	59	73.0	0.808	0.00000380	786
Loss of Function	0.313	16	17.4	0.919	7.31e-7	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000369	0.000367
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000220	0.000217
Finnish	0.000375	0.000370
European (Non-Finnish)	0.000363	0.000352
Middle Eastern	0.000220	0.000217
South Asian	0.000626	0.000588
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the transport of adenosine 3'-phospho 5'- phosphosulfate (PAPS), from cytosol into Golgi. PAPS is a universal sulfuryl donor for sulfation events that take place in the Golgi. Compensates for the insufficient expression of SLC35B2/PAPST1 during the synthesis of sulfated glycoconjugates in the colon. {ECO:0000269|PubMed:16492677}.
• Pathway: Transport and synthesis of PAPS;Metabolism of carbohydrates;Phase II - Conjugation of compounds;Glycosaminoglycan metabolism;Biological oxidations;Metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Cytosolic sulfonation of small molecules;Transport of nucleotide sugars (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.867
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.294
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.226

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc35b3

Gene ontology

• Biological process: 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process;3'-phospho-5'-adenylyl sulfate transmembrane transport
• Cellular component: Golgi membrane;integral component of Golgi membrane;integral component of endoplasmic reticulum membrane
• Molecular function: transmembrane transporter activity;3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity