SLC35F3

protein-coding

solute carrier family 35 member F3, the group of Solute carrier family 35|MicroRNA protein coding host genes

Gene summary

Enables choline transmembrane transporter activity. Involved in choline transport and thiamine transport. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_173508.4

Inheritance

—

ClinVar variants

U:66B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr1:233,904,676-234,324,511

External References & Databases

Ensembl (ENSG00000183780)

Transcript & Mutation Effects

hg38 • Region Span ~419.8 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 SLC35F3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173508.4. 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			1 clinvar	2 clinvar	1 clinvar	4
missense			65 clinvar	2 clinvar	1 clinvar	68
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	66	4	2	72

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173508.4	RefSeq	NP_775779.1	8	MANE Select
ENST00000366618.8	Ensembl	ENSP00000355577.3	8	MANE Select
NM_001300845.2	RefSeq	NP_001287774.1	7	Standard
ENST00000366617.3	Ensembl	ENSP00000355576.3	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

thiamine transport

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000366618
Coding exons: 8
Length: 419584
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125748
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.71	220	304	0.724	0.0000183	3160
Missense (PolyPhen)		84	130.38	0.64429		1447
Synonymous	-0.0671	137	136	1.01	0.00000952	1006
Loss of Function	3.18	6	22.1	0.271	0.00000115	241

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be a thiamine transporter. {ECO:0000303|PubMed:24509276}.;

Recessive Scores

pRec: 0.0785

Intolerance Scores

LoFtool: 0.161
RVIS EVS: -0.62
RVIS percentile EVS: 17.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.160

Gene Damage Prediction

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