SLC44A5

protein-coding

solute carrier family 44 member 5, the group of Solute carrier family 44

Gene summary

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

MANE transcript

NM_001130058.2

Inheritance

—

ClinVar variants

U:74B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr1:75,202,129-75,611,114

External References & Databases

Ensembl (ENSG00000137968)

Transcript & Mutation Effects

hg38 • Region Span ~409.0 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 SLC44A5 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 77

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001130058.2. 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						0
missense			67 clinvar	6 clinvar		73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	74	6	0	80

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001130058.2	RefSeq	NP_001123530.1	23	MANE Select
ENST00000370859.8	Ensembl	ENSP00000359896.3	23	MANE Select
NM_001320283.3	RefSeq	NP_001307212.1	22	Standard
NM_001320285.2	RefSeq	NP_001307214.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Choline metabolism in cancer - Homo sapiens (human)
Metabolism of lipids
Amine compound SLC transporters
Metabolism
Transport of bile salts and organic acids, metal ions and amine compounds

Biological Process

phosphatidylcholine biosynthetic process
choline transport
transmembrane transport

Molecular Function

choline transmembrane transporter activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370855
Coding exons: 23
Length: 408986
Individuals with no LoFs: 125705
Homozygous LoFs: 0
Heterozygous LoFs: 40
Defined: 125745
p: 0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.18	314	379	0.830	0.0000186	4715
Missense (PolyPhen)		80	128.04	0.62478		1696
Synonymous	0.0531	131	132	0.994	0.00000657	1327
Loss of Function	4.17	16	46.8	0.342	0.00000253	548

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.00051	0.00051	rare
European (Non-Finnish)	0.00017	0.00016	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0966

Intolerance Scores

LoFtool: 0.679
RVIS EVS: -0.29
RVIS percentile EVS: 33.34

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0965

Gene Damage Prediction

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