SLC25A45

protein-coding

solute carrier family 25 member 45, the group of Solute carrier family 25

Gene summary

Enables N(6),N(6),N(6)-trimethyl-L-lysine transmembrane transporter activity and dimethylarginine transmembrane transporter activity. Involved in carnitine biosynthetic process. Is active in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_182556.4

Inheritance

—

ClinVar variants

U:48B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr11:65,375,192-65,383,701

External References & Databases

Ensembl (ENSG00000162241)

Transcript & Mutation Effects

hg38 • Region Span ~8.5 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 SLC25A45 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182556.4. 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				2 clinvar		2
missense			48 clinvar	3 clinvar		51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	5	0	53

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182556.4	RefSeq	NP_872362.4	6	MANE Select
ENST00000398802.6	Ensembl	ENSP00000381782.1	6	MANE Select
NM_001077241.3	RefSeq	NP_001070709.3	4	Standard
NM_001278250.3	RefSeq	NP_001265179.3	5	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

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: ENST00000398802
Coding exons: 6
Length: 8510
Individuals with no LoFs: 124565
Homozygous LoFs: 0
Heterozygous LoFs: 236
Defined: 124801
p: 0.000946

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.134	178	183	0.972	0.0000116	1839
Missense (PolyPhen)		71	77.592	0.91504		823
Synonymous	0.329	72	75.6	0.952	0.00000454	614
Loss of Function	0.600	11	13.4	0.823	7.55e-7	134

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0083	0.0083	notable
Latino/Admixed American	0.0012	0.0012	notable
Ashkenazi Jewish	0.00090	0.00089	rare
East Asian	0.00045	0.00045	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00035	0.00034	rare
South Asian	0.00023	0.00023	rare
Other	0.00083	0.00082	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0696

Intolerance Scores

LoFtool: 0.546
RVIS EVS: 1.55
RVIS percentile EVS: 95.62

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00353

Gene Damage Prediction

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