SLC29A1

solute carrier family 29 member 1 (Augustine blood group), the group of Solute carrier family 29|Blood group antigens

Basic information

Region (hg38): 6:44219553-44234142

Previous symbols: [ "ENT1" ]

Links

ENSG00000112759 ∙ NCBI:2030 ∙ OMIM:602193 ∙ HGNC:11003 ∙ Uniprot:Q99808 ∙ 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 SLC29A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC29A1 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	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding				1	1	2
Total	0	0	12	3	2

Variants in SLC29A1

This is a list of pathogenic ClinVar variants found in the SLC29A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-44221578-T-A		SLC29A1-related disorder	Likely benign (Jun 01, 2023)
6-44223649-C-T		SLC29A1-related disorder	Likely benign (May 30, 2023)
6-44227333-C-T		Squamous cell carcinoma of the head and neck	Uncertain significance (Jul 19, 2019)
6-44229444-G-A			Benign (Nov 20, 2018)
6-44229671-C-T		not specified	Uncertain significance (Nov 08, 2022)
6-44229917-T-C		not specified	Uncertain significance (Apr 20, 2024)
6-44229918-C-T		not specified	Uncertain significance (Jul 11, 2023)
6-44230032-T-C		not specified	Uncertain significance (Feb 22, 2023)
6-44230033-C-G		not specified	Uncertain significance (Dec 16, 2023)
6-44230034-G-A		not specified	Likely benign (Feb 02, 2022)
6-44230457-G-A		not specified	Uncertain significance (Oct 26, 2022)
6-44230559-C-T			Benign (Jun 14, 2018)
6-44230596-C-T			Likely benign (Aug 14, 2018)
6-44230639-A-G		not specified	Uncertain significance (Apr 06, 2024)
6-44230651-G-A		not specified	Uncertain significance (Aug 17, 2021)
6-44231359-C-T			Benign (Jun 14, 2018)
6-44231465-C-T			Benign (Jun 05, 2018)
6-44232035-C-A		not specified	Uncertain significance (Apr 19, 2023)
6-44232346-G-A		not specified	Uncertain significance (May 31, 2022)
6-44232398-G-C		not specified	Uncertain significance (May 06, 2024)
6-44232834-A-G		not specified	Uncertain significance (Nov 08, 2022)
6-44232894-C-T		not specified	Uncertain significance (Jan 24, 2024)
6-44232906-A-C		Hemolytic disease of fetus OR newborn due to isoimmunization	Pathogenic (May 20, 2017)
6-44232952-C-T		not specified	Uncertain significance (Jun 03, 2022)
6-44233410-C-T			Likely benign (Jan 17, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC29A1	protein_coding	protein_coding	ENST00000393841	12	14647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.901	0.0993	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.720	228	261	0.875	0.0000153	2952
Missense in Polyphen		71	104.15	0.68173		1194
Synonymous	0.744	97	107	0.908	0.00000647	954
Loss of Function	3.60	3	20.7	0.145	8.83e-7	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000911	0.0000911
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000727	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates both influx and efflux of nucleosides across the membrane (equilibrative transporter). It is sensitive (ES) to low concentrations of the inhibitor nitrobenzylmercaptopurine riboside (NBMPR) and is sodium-independent. It has a higher affinity for adenosine. Inhibited by dipyridamole and dilazep (anticancer chemotherapeutics drugs).
• Pathway: Alcoholism - Homo sapiens (human);Fluoropyrimidine Pathway, Pharmacokinetics;Gemcitabine Pathway, Pharmacodynamics;Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Thioguanine Action Pathway;Gemcitabine Action Pathway;Mercaptopurine Metabolism Pathway;Gemcitabine Metabolism Pathway;Fluoropyrimidine Activity;Purine metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Pyrimidine metabolism;Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane (Consensus)

Recessive Scores

• pRec: 0.222

Intolerance Scores

• loftool: 0.513
• rvis_EVS: 0.57
• rvis_percentile_EVS: 82.08

Haploinsufficiency Scores

• pHI: 0.513
• hipred: Y
• hipred_score: 0.518
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.859

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc29a1
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype

Gene ontology

• Biological process: nucleobase-containing compound metabolic process;lactation;nucleoside transport;uridine transport;sleep;excitatory postsynaptic potential;cellular response to glucose stimulus;cellular response to hypoxia;neurotransmitter reuptake;nucleoside transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;basolateral plasma membrane;apical plasma membrane;presynapse;postsynapse
• Molecular function: nucleoside transmembrane transporter activity