SLC44A2

solute carrier family 44 member 2, the group of Solute carrier family 44

Basic information

Region (hg38): 19:10602457-10644557

Links

ENSG00000129353NCBI:57153OMIM:606106HGNC:17292Uniprot:Q8IWA5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC44A2 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
missense
83
clinvar
5
clinvar
88
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 83 5 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC44A2protein_codingprotein_codingENST00000335757 2242103
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0001191.001257150331257480.000131
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9773674240.8660.00002744620
Missense in Polyphen94119.880.784121299
Synonymous-0.09981751731.010.00001191380
Loss of Function3.721439.10.3580.00000184462

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001750.000175
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001420.000132
Middle Eastern0.000.00
South Asian0.0003290.000327
Other0.0003260.000326

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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