SLC44A2

protein-coding

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

Gene summary

Enables choline transmembrane transporter activity and ethanolamine transmembrane transporter activity. Involved in choline transport; ethanolamine transport; and transmembrane transport. Located in mitochondrial outer membrane and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020428.4

Inheritance

—

ClinVar variants

U:114B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr19:10,602,457-10,644,557

External References & Databases

Ensembl (ENSG00000129353)

Transcript & Mutation Effects

hg38 • Region Span ~42.1 kb

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GenCC 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 SLC44A2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 96

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020428.4. 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			1 clinvar		2 clinvar	3
missense			101 clinvar	5 clinvar		106
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			11 clinvar			11
Total	0	0	114	5	2	121

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020428.4	RefSeq	NP_065161.3	22	MANE Select
ENST00000335757.10	Ensembl	ENSP00000336888.4	22	MANE Select
NM_001145056.2	RefSeq	NP_001138528.1	22	Standard
NM_001363611.2	RefSeq	NP_001350540.1	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Choline metabolism in cancer - Homo sapiens (human)
sarcosine oncometabolite pathway
Neutrophil degranulation
Metabolism of lipids
Amine compound SLC transporters

Biological Process

phosphatidylcholine biosynthetic process
choline transport
positive regulation of I-kappaB kinase/NF-kappaB signaling
neutrophil degranulation
transmembrane transport

Molecular Function

choline transmembrane transporter activity

Cellular Component

lysosomal membrane
plasma membrane
integral component of membrane
specific granule membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335757
Coding exons: 22
Length: 42103
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125748
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.977	367	424	0.866	0.0000274	4620
Missense (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

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	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.00013	rare
South Asian	0.00033	0.00033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Isoform 1, but not isoform 3, exhibits some choline transporter activity. {ECO:0000269|PubMed:10677542, ECO:0000269|PubMed:20665236}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.581
RVIS EVS: -0.93
RVIS percentile EVS: 9.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.170

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium