SLC25A48

protein-coding

solute carrier family 25 member 48, the group of Solute carrier family 25

Gene summary

Enables choline transmembrane transporter activity. Involved in choline transport. Located in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001349336.2

Inheritance

—

ClinVar variants

U:20B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr5:135,476,913-135,889,770

External References & Databases

Ensembl (ENSG00000145832)

Transcript & Mutation Effects

hg38 • Region Span ~412.9 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 SLC25A48 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 20

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001349336.2. 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			1 clinvar	1 clinvar		2
missense			18 clinvar	2 clinvar		20
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	20	3	0	23

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 65 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001349336.2	RefSeq	NP_001336265.1	7	MANE Select
ENST00000681962.1	Ensembl	ENSP00000506858.1	7	MANE Select
NM_001349335.2	RefSeq	NP_001336264.1	4	Standard
NM_001349345.2	RefSeq	NP_001336274.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

acyl carnitine transport
acyl carnitine transmembrane transport

Molecular Function

protein binding
acyl carnitine transmembrane transporter activity

Cellular Component

mitochondrial inner membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000412661
Coding exons: 5
Length: 53989
Individuals with no LoFs: 124752
Homozygous LoFs: 0
Heterozygous LoFs: 26
Defined: 124778
p: 0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.787	86	109	0.788	0.00000722	1023
Missense (PolyPhen)		28	38.484	0.72758		397
Synonymous	0.605	39	44.1	0.884	0.00000306	318
Loss of Function	0.236	6	6.66	0.901	2.83e-7	74

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000082	0.000065	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00050	0.00045	rare
Finnish	0.00017	0.00014	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.53
RVIS percentile EVS: 80.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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