SLC29A1

protein-coding

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

Gene summary

This gene is a member of the equilibrative nucleoside transporter family. The gene encodes a transmembrane glycoprotein that localizes to the plasma and mitochondrial membranes and mediates the cellular uptake of nucleosides from the surrounding medium. The protein is categorized as an equilibrative (as opposed to concentrative) transporter that is sensitive to inhibition by nitrobenzylthioinosine (NBMPR). Nucleoside transporters are required for nucleotide synthesis in cells that lack de novo nucleoside synthesis pathways, and are also necessary for the uptake of cytotoxic nucleosides used for cancer and viral chemotherapies. Multiple alternatively spliced variants, encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008]

Previous symbols:

ENT1

MANE transcript

NM_001372327.1

Inheritance

—

ClinVar variants

P:1U:50B:5

Top phenotype

Hemolytic disease of fetus OR newborn due to isoimmunization

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr6:44,219,553-44,234,142

External References & Databases

Ensembl (ENSG00000112759)

Transcript & Mutation Effects

hg38 • Region Span ~14.6 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 SLC29A1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 8

Hemolytic disease of fetus OR newborn due to isoimmunizationTotal: 1

SLC29A1-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001372327.1. 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			2 clinvar	1 clinvar	1 clinvar	4
missense	1 clinvar		44 clinvar	3 clinvar		48
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	1	0	50	4	1	56

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 239 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001372327.1	RefSeq	NP_001359256.1	12	MANE Select
ENST00000371755.9	Ensembl	ENSP00000360820.3	12	MANE Select
NM_001078175.3	RefSeq	NP_001071643.1	12	Standard
NM_001078177.2	RefSeq	NP_001071645.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Alcoholism - Homo sapiens (human)
Fluoropyrimidine Pathway, Pharmacokinetics
Gemcitabine Pathway, Pharmacodynamics
Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics
Mercaptopurine Action Pathway

Biological Process

nucleobase-containing compound metabolic process
lactation
nucleoside transport
uridine transport
sleep

Molecular Function

nucleoside transmembrane transporter activity

Cellular Component

plasma membrane
integral component of plasma membrane
membrane
basolateral plasma membrane
apical plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393841
Coding exons: 12
Length: 14647
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125748
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.720	228	261	0.875	0.0000153	2952
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000073	0.000070	rare
South Asian	0.00023	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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).;

Recessive Scores

pRec: 0.222

Intolerance Scores

LoFtool: 0.513
RVIS EVS: 0.57
RVIS percentile EVS: 82.08

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.859

Gene Damage Prediction

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