SLC44A2

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

Basic information

Region (hg38): 19:10602457-10644557

Links

ENSG00000129353 ∙ NCBI:57153 ∙ OMIM:606106 ∙ HGNC:17292 ∙ Uniprot:Q8IWA5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			47	5		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	48	5	2

Variants in SLC44A2

This is a list of pathogenic ClinVar variants found in the SLC44A2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-10625637-G-T		not specified	Uncertain significance (Dec 04, 2024)
19-10625638-G-A		not specified	Uncertain significance (Jan 09, 2025)
19-10625644-A-G		not specified	Uncertain significance (Jan 20, 2025)
19-10626255-A-G		not specified	Uncertain significance (Mar 28, 2024)
19-10626262-A-T		not specified	Uncertain significance (Aug 13, 2021)
19-10627750-T-A		not specified	Uncertain significance (Jul 27, 2022)
19-10627777-G-A		not specified	Uncertain significance (Apr 08, 2022)
19-10631305-C-T		not specified	Uncertain significance (Jun 22, 2021)
19-10631374-A-C		not specified	Likely benign (May 26, 2022)
19-10631490-C-T			Likely benign (Jan 01, 2023)
19-10631631-C-T		not specified	Uncertain significance (Dec 20, 2024)
19-10631632-G-A		not specified	Likely benign (Apr 13, 2022)
19-10631632-G-C		not specified	Uncertain significance (Dec 26, 2023)
19-10631641-T-G		not specified	Uncertain significance (Dec 19, 2023)
19-10631663-G-T		not specified	Uncertain significance (Aug 27, 2024)
19-10631668-T-C		not specified	Uncertain significance (Mar 18, 2024)
19-10631715-C-T		not specified	Uncertain significance (Mar 01, 2023)
19-10631716-G-A		not specified	Uncertain significance (Jul 02, 2024)
19-10631930-T-A		not specified	Uncertain significance (Dec 17, 2023)
19-10632085-T-C		not specified	Uncertain significance (Nov 17, 2022)
19-10632142-T-C		not specified	Uncertain significance (Feb 22, 2025)
19-10634773-A-G		not specified	Uncertain significance (Dec 20, 2023)
19-10634803-G-A		not specified	Uncertain significance (Dec 20, 2023)
19-10634848-C-T		not specified	Uncertain significance (Dec 13, 2023)
19-10634867-G-A		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

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: 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

	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