SLC16A9

protein-coding

solute carrier family 16 member 9, the group of Solute carrier family 16

Gene summary

Enables carnitine transmembrane transporter activity and creatine transmembrane transporter activity. Involved in carnitine transmembrane transport; creatine transmembrane transport; and urate metabolic process. Located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C10orf36

MANE transcript

NM_194298.3

Inheritance

—

ClinVar variants

U:59B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr10:59,650,764-59,736,002

External References & Databases

Ensembl (ENSG00000165449)

Transcript & Mutation Effects

hg38 • Region Span ~85.2 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 SLC16A9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 56

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_194298.3. 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
missense			56 clinvar	2 clinvar	1 clinvar	59
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	59	2	2	63

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 61 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_194298.3	RefSeq	NP_919274.1	5	MANE Select
ENST00000395348.8	Ensembl	ENSP00000378757.3	5	MANE Select
NM_001323977.1	RefSeq	NP_001310906.1	4	Standard
NM_001323978.2	RefSeq	NP_001310907.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycosphingolipid metabolism
Glycerophospholipid metabolism

Biological Process

monocarboxylic acid transport
urate metabolic process
transmembrane transport

Molecular Function

protein binding
monocarboxylic acid transmembrane transporter activity
symporter activity

Cellular Component

integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395348
Coding exons: 5
Length: 85238
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 125748
p: 0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.701	232	264	0.879	0.0000129	3282
Missense (PolyPhen)		78	95.562	0.81622		1147
Synonymous	-0.334	110	106	1.04	0.00000592	1029
Loss of Function	2.58	7	19.2	0.364	9.00e-7	261

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000098	0.000097	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Proton-linked monocarboxylate transporter. May catalyze the transport of monocarboxylates across the plasma membrane. {ECO:0000250}.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.458
RVIS EVS: 0.49
RVIS percentile EVS: 79.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.333

Gene Damage Prediction

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