SLC44A2
Basic information
Region (hg38): 19:10602457-10644557
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (86 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC44A2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020428.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 83 | 88 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 83 | 5 | 2 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC44A2 | protein_coding | protein_coding | ENST00000335757 | 22 | 42103 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000119 | 1.00 | 125715 | 0 | 33 | 125748 | 0.000131 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.977 | 367 | 424 | 0.866 | 0.0000274 | 4620 |
| Missense in Polyphen | 94 | 119.88 | 0.78412 | 1299 | ||
| Synonymous | -0.0998 | 175 | 173 | 1.01 | 0.0000119 | 1380 |
| Loss of Function | 3.72 | 14 | 39.1 | 0.358 | 0.00000184 | 462 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000175 | 0.000175 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000142 | 0.000132 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000329 | 0.000327 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Isoform 1, but not isoform 3, exhibits some choline transporter activity. {ECO:0000269|PubMed:10677542, ECO:0000269|PubMed:20665236}.;
- Pathway
- Choline metabolism in cancer - Homo sapiens (human);sarcosine oncometabolite pathway ;Neutrophil degranulation;Metabolism of lipids;Amine compound SLC transporters;Innate Immune System;Immune System;Metabolism;Transport of bile salts and organic acids, metal ions and amine compounds;Synthesis of PC;SLC-mediated transmembrane transport;Transport of small molecules;Glycerophospholipid biosynthesis;Phospholipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.581
- rvis_EVS
- -0.93
- rvis_percentile_EVS
- 9.68
Haploinsufficiency Scores
- pHI
- 0.259
- hipred
- Y
- hipred_score
- 0.554
- ghis
- 0.546
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.170
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc44a2
- Phenotype
- growth/size/body region phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype;
Gene ontology
- Biological process
- phosphatidylcholine biosynthetic process;choline transport;positive regulation of I-kappaB kinase/NF-kappaB signaling;neutrophil degranulation;transmembrane transport
- Cellular component
- lysosomal membrane;plasma membrane;integral component of membrane;specific granule membrane;extracellular exosome
- Molecular function
- choline transmembrane transporter activity