SLC35F3

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

Basic information

Region (hg38): 1:233904675-234324511

Links

ENSG00000183780 ∙ NCBI:148641 ∙ ∙ HGNC:23616 ∙ Uniprot:Q8IY50 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC35F3 gene.

• Inborn genetic diseases (13 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC35F3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			12	2	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	12	3	3

Variants in SLC35F3

This is a list of pathogenic ClinVar variants found in the SLC35F3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-233905102-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-233905670-C-A		not specified	Uncertain significance (Jul 26, 2022)
1-234231438-C-G		not specified	Uncertain significance (Jan 31, 2024)
1-234231492-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-234231497-C-T		not specified	Uncertain significance (May 23, 2023)
1-234231501-G-A		not specified	Uncertain significance (Feb 09, 2023)
1-234231518-C-G			Benign (Feb 25, 2021)
1-234231530-A-G		not specified	Uncertain significance (Jan 03, 2024)
1-234231548-G-A			Likely benign (May 08, 2018)
1-234231548-G-T		not specified	Uncertain significance (Dec 28, 2023)
1-234231566-G-C		not specified	Uncertain significance (Aug 17, 2021)
1-234231657-A-G		not specified	Uncertain significance (Sep 21, 2023)
1-234231702-G-T		not specified	Uncertain significance (Feb 22, 2024)
1-234316592-G-A			Benign (Mar 29, 2018)
1-234316650-G-C		not specified	Uncertain significance (Apr 12, 2022)
1-234318782-A-G		not specified	Uncertain significance (Jul 26, 2022)
1-234318853-A-G		not specified	Likely benign (Dec 15, 2022)
1-234318931-G-T		not specified	Uncertain significance (Nov 10, 2022)
1-234320107-T-C		not specified	Uncertain significance (Sep 26, 2023)
1-234320130-G-A		not specified	Uncertain significance (Nov 07, 2022)
1-234323030-G-C		not specified	Uncertain significance (Jan 31, 2024)
1-234323041-A-G		not specified	Uncertain significance (Feb 28, 2023)
1-234323108-G-A			Benign (May 08, 2018)
1-234323178-G-A		not specified	Uncertain significance (Mar 22, 2023)
1-234323231-C-T			Likely benign (May 03, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC35F3	protein_coding	protein_coding	ENST00000366618	8	419584

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0996	0.900	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.71	220	304	0.724	0.0000183	3160
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000122	0.000120
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.149
• hipred: Y
• hipred_score: 0.741
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc35f3

Gene ontology

• Biological process: thiamine transport
• Cellular component: integral component of membrane