SLC35G1
protein-codingsolute carrier family 35 member G1, the group of Solute carrier family 35
Gene summary
This gene encodes a transmembrane protein which is a member of the drug/metabolite transporter protein superfamily. The encoded protein may play a role in the regulation of calcium levels inside the cell. [provided by RefSeq, Sep 2016]
- TMEM20
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~62.1 kbGenCC 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 SLC35G1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001134658.3. 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 | 2 | 1 | 3 | |||
| missense | 54 | 5 | 59 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 57 | 6 | 0 | 63 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001128130.1 | 3 | MANE Select | |
| Ensembl | ENSP00000400932.1 | 3 | MANE Select | |
| RefSeq | NP_001332922.1 | 3 | Standard | |
| RefSeq | NP_694958.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of cytosolic calcium ion concentration
- calcium ion export across plasma membrane
Molecular Function
- protein binding
Cellular Component
- endoplasmic reticulum membrane
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000427197
- Coding exons
- 3
- Length
- 62090
- Individuals with no LoFs
- 125678
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 59
- Defined
- 125737
- p
- 0.000235
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0131 | 191 | 192 | 0.997 | 0.0000101 | 2351 |
| Missense (PolyPhen) | 44 | 56.902 | 0.77326 | 683 | ||
| Synonymous | 0.918 | 65 | 75.1 | 0.865 | 0.00000456 | 756 |
| Loss of Function | 2.13 | 3 | 10.4 | 0.288 | 6.03e-7 | 136 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00028 | 0.00026 | rare |
| Ashkenazi Jewish | 0.0024 | 0.0021 | notable |
| East Asian | 0.00039 | 0.00038 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000091 | 0.000088 | rare |
| South Asian | 0.00017 | 0.00016 | rare |
| Other | 0.00053 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role in intracellular calcium sensing and homeostasis. May act as a negative regulator of plasma membrane calcium-transporting ATPases preventing calcium efflux from the cell. {ECO:0000269|PubMed:22084111}.;
Recessive Scores
- pRec
- 0.0305
Intolerance Scores
- RVIS EVS
- -0.43
- RVIS percentile EVS
- 25.15
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |