SLC44A1

protein-coding

solute carrier family 44 member 1, the group of Solute carrier family 44|CD molecules

Gene summary

Enables choline transmembrane transporter activity and ethanolamine transmembrane transporter activity. Involved in choline transport; ethanolamine transport; and transmembrane transport. Located in cytosol; mitochondrial outer membrane; and plasma membrane. Implicated in high grade glioma. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CDW92

MANE transcript

NM_080546.5

Inheritance

ClinVar variants

P:7U:107B:15

Top phenotype

Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr9:105,244,622-105,439,171

External References & Databases

Ensembl (ENSG00000070214)

Transcript & Mutation Effects

hg38 • Region Span ~194.5 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive declineMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0030028

Submitter: Ambry Genetics

neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive declineSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030028

Submitter: PanelApp Australia

neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive declineSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030028

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive declineAR

Manifestation: Neurologic; Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Comments: Oral choline treatment did not appear to be beneficial

Refs: 28097321; 31855247

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC44A1 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 96

not providedTotal: 14

SLC44A1-related disorderTotal: 12

Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive declineTotal: 4

Neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080546.5. 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	8 clinvar	2 clinvar	11
missense			94 clinvar	4 clinvar	1 clinvar	99
nonsense	1 clinvar	2 clinvar	2 clinvar			5
start loss						0
frameshift	3 clinvar					3
splice donor/acceptor (+/-2bp)		1 clinvar	10 clinvar			11
Total	4	3	107	12	3	129

Highest pathogenic variant AF is 0.000006573844

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 78 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080546.5	RefSeq	NP_536856.2	16	MANE Select
ENST00000374720.8	Ensembl	ENSP00000363852.3	16	MANE Select
NM_001286730.2	RefSeq	NP_001273659.1	16	Standard
NM_001330731.2	RefSeq	NP_001317660.1	16	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
Metabolism of lipids
Amine compound SLC transporters
Metabolism of amino acids and derivatives

Biological Process

phosphatidylcholine biosynthetic process
choline transport
choline catabolic process
transmembrane transport

Molecular Function

choline transmembrane transporter activity

Cellular Component

nucleoplasm
mitochondrion
mitochondrial outer membrane
plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374720
Coding exons: 16
Length: 194550
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125747
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.73	260	351	0.740	0.0000181	4269
Missense (PolyPhen)		72	127.55	0.56448		1639
Synonymous	0.385	122	128	0.957	0.00000660	1292
Loss of Function	4.81	4	34.5	0.116	0.00000182	421

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000077	0.000062	rare
Latino/Admixed American	0.000090	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000072	0.000070	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Choline transporter. May be involved in membrane synthesis and myelin production. {ECO:0000269|PubMed:19357133}.;

Recessive Scores

pRec: 0.137

Intolerance Scores

LoFtool: 0.274
RVIS EVS: -0.53
RVIS percentile EVS: 20.7

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.183

Gene Damage Prediction

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