SLC35B2
protein-codingsolute carrier family 35 member B2, the group of MicroRNA protein coding host genes|Solute carrier family 35
Gene summary
Sulfotransferases (e.g., SULT4A1; MIM 608359) use an activated form of sulfate, 3-prime-phosphoadenosine 5-prime-phosphosulfate (PAPS), as a common sulfate donor for sulfation of glycoproteins, proteoglycans, and glycolipids in the endoplasmic reticulum and Golgi apparatus. SLC35B2 is located in the microsomal membrane and transports PAPS from the cytosol, where it is synthesized, into the Golgi lumen (Kamiyama et al., 2003 [PubMed 12716889]).[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0859518
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0859518
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0859518
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0859518
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Musculoskeletal; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC35B2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_178148.4. 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 | 3 | 1 | 4 | |||
| missense | 84 | 3 | 1 | 88 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | 4 | |||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 2 | 0 | 88 | 6 | 2 | 98 |
Highest pathogenic variant AF is 0.000051436567
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_835361.1 | 4 | MANE Select | |
| Ensembl | ENSP00000377401.3 | 4 | MANE Select | |
| RefSeq | NP_001273438.1 | 3 | Standard | |
| RefSeq | NP_001273439.1 | 3 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| slc35b2 | Danio rerio | Structure: retinal ganglion cell Quality: organization quality abnormal |
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
- positive regulation of I-kappaB kinase/NF-kappaB signaling
- 3'-phosphoadenosine 5'-phosphosulfate transport
- 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
- Golgi apparatus
- membrane
- integral component of membrane
- integral component of Golgi membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000393812
- Coding exons
- 4
- Length
- 3459
- Individuals with no LoFs
- 125701
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 47
- Defined
- 125748
- p
- 0.000187
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.261 | 263 | 251 | 1.05 | 0.0000141 | 2748 |
| Missense (PolyPhen) | 72 | 81.672 | 0.88158 | 985 | ||
| Synonymous | -2.37 | 137 | 106 | 1.29 | 0.00000574 | 961 |
| Loss of Function | 2.66 | 5 | 16.7 | 0.299 | 9.15e-7 | 162 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00017 | 0.00017 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00069 | 0.00069 | rare |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- 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. May indirectly participate in activation of the NF- kappa-B and MAPK pathways. {ECO:0000269|PubMed:12716889}.;
Intolerance Scores
- LoFtool
- 0.698
- RVIS EVS
- -0.82
- RVIS percentile EVS
- 11.77
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.911
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |