SLC35B3

protein-coding

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

Gene summary

This gene is a member of the solute carrier family. The encoded protein is involved in the transport of 3-prime phosphoadenosine 5-prime phosphosulfate (PAPS) from the nucleus or the cytosol to the Golgi lumen. This gene has been reported to be expressed preferentially in the human colon tissues. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

Previous symbols:

C6orf196

MANE transcript

NM_001370479.2

Inheritance

—

ClinVar variants

U:42B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.92

Max pathogenic AF

—

Genomic locus

chr6:8,411,435-8,435,561

External References & Databases

Ensembl (ENSG00000124786)

Transcript & Mutation Effects

hg38 • Region Span ~24.1 kb

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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 SLC35B3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 42

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370479.2. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			39 clinvar	3 clinvar		42
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	42	3	0	45

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 111 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001370479.2	RefSeq	NP_001357408.1	9	MANE Select
ENST00000710437.1	Ensembl	ENSP00000518269.1	9	MANE Select
NM_001142540.2	RefSeq	NP_001136012.1	10	Standard
NM_001142541.3	RefSeq	NP_001136013.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transport and synthesis of PAPS
Metabolism of carbohydrates
Phase II - Conjugation of compounds
Glycosaminoglycan metabolism
Biological oxidations

Biological Process

3'-phosphoadenosine 5'-phosphosulfate biosynthetic process
3'-phospho-5'-adenylyl sulfate transmembrane transport

Molecular Function

transmembrane transporter activity
3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity

Cellular Component

Golgi membrane
integral component of Golgi membrane
integral component of endoplasmic reticulum membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379660
Coding exons: 10
Length: 22494
Individuals with no LoFs: 125666
Homozygous LoFs: 0
Heterozygous LoFs: 81
Defined: 125747
p: 0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.501	184	204	0.901	0.00000990	2594
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.00036	0.00035	rare
South Asian	0.00063	0.00059	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.867
RVIS EVS: -0.2
RVIS percentile EVS: 38.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.226

Gene Damage Prediction

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