SLC45A4

protein-coding

solute carrier family 45 member 4, the group of Solute carrier family 45

Gene summary

Enables putrescine transmembrane transporter activity; spermidine transmembrane transporter activity; and spermine transmembrane transporter activity. Involved in sensory perception of pain. Is active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001286646.2

Inheritance

—

ClinVar variants

U:162B:28

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr8:141,207,166-141,308,305

External References & Databases

Ensembl (ENSG00000022567)

Transcript & Mutation Effects

hg38 • Region Span ~101.1 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 SLC45A4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 173

not providedTotal: 16

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001286646.2. 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			6 clinvar	2 clinvar	9 clinvar	17
missense			154 clinvar	14 clinvar	3 clinvar	171
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	162	16	12	190

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001286646.2	RefSeq	NP_001273575.1	8	MANE Select
ENST00000517878.6	Ensembl	ENSP00000428137.1	8	MANE Select
NM_001080431.3	RefSeq	NP_001073900.1	8	Standard
NM_001286648.2	RefSeq	NP_001273577.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

sucrose transport

Molecular Function

sucrose:proton symporter activity

Cellular Component

membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000024061
Coding exons: 8
Length: 101140
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125748
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.833	486	540	0.899	0.0000393	5137
Missense (PolyPhen)		119	158.76	0.74954		1527
Synonymous	-1.41	275	247	1.11	0.0000206	1655
Loss of Function	2.67	11	25.5	0.431	0.00000118	273

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0.000065	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0935

Intolerance Scores

LoFtool: 0.127
RVIS EVS: -1.3
RVIS percentile EVS: 4.99

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.808

Gene Damage Prediction

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