SLC29A2

solute carrier family 29 member 2, the group of Solute carrier family 29

Basic information

Region (hg38): 11:66362521-66372214

Previous symbols: [ "ENT2", "HNP36" ]

Links

ENSG00000174669 ∙ NCBI:3177 ∙ OMIM:602110 ∙ HGNC:11004 ∙ Uniprot:Q14542 ∙ 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 SLC29A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC29A2 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						0
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in SLC29A2

This is a list of pathogenic ClinVar variants found in the SLC29A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66363470-G-T		not specified	Uncertain significance (Dec 16, 2023)
11-66363516-C-T		not specified	Uncertain significance (Jan 03, 2024)
11-66364286-T-C		not specified	Uncertain significance (Aug 22, 2023)
11-66364346-C-T		not specified	Uncertain significance (Nov 02, 2023)
11-66364408-C-T		not specified	Uncertain significance (Feb 23, 2023)
11-66364409-G-A		not specified	Uncertain significance (Jun 12, 2023)
11-66366171-C-T		not specified	Uncertain significance (Oct 25, 2022)
11-66366180-C-T		not specified	Uncertain significance (Feb 28, 2023)
11-66366466-G-C		not specified	Uncertain significance (Apr 09, 2024)
11-66366557-G-T		not specified	Uncertain significance (Dec 18, 2023)
11-66367477-C-G		not specified	Uncertain significance (Jun 21, 2022)
11-66367508-G-A		not specified	Uncertain significance (Jun 13, 2023)
11-66367852-T-A		not specified	Uncertain significance (Jun 02, 2023)
11-66367855-C-T		not specified	Uncertain significance (Mar 17, 2023)
11-66367866-C-T		not specified	Uncertain significance (Nov 28, 2023)
11-66368548-A-C		not specified	Uncertain significance (Mar 08, 2024)
11-66368554-A-G		not specified	Uncertain significance (Feb 23, 2023)
11-66368602-A-T		not specified	Uncertain significance (Dec 14, 2021)
11-66368608-C-G		not specified	Uncertain significance (Jun 11, 2021)
11-66369080-G-A		not specified	Uncertain significance (Feb 17, 2024)
11-66369081-C-A		not specified	Uncertain significance (Feb 17, 2024)
11-66369104-C-G		not specified	Uncertain significance (Jan 26, 2023)
11-66369182-C-T		not specified	Uncertain significance (Apr 20, 2023)
11-66369468-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-66369522-G-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC29A2	protein_coding	protein_coding	ENST00000357440	12	9694

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.23e-14	0.0210	125658	0	90	125748	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.481	236	258	0.916	0.0000155	2924
Missense in Polyphen		89	106.37	0.83668		1235
Synonymous	1.46	102	123	0.832	0.00000829	977
Loss of Function	0.0846	21	21.4	0.980	0.00000102	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000537	0.000536
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000601	0.000598
Middle Eastern	0.000163	0.000163
South Asian	0.0000662	0.0000653
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates equilibrative transport of purine, pyrimidine nucleosides and the purine base hypoxanthine. Very less sensitive than SLC29A1 to inhibition by nitrobenzylthioinosine (NBMPR), dipyridamole, dilazep and draflazine. {ECO:0000269|PubMed:9396714}.
• Pathway: Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Thioguanine Action Pathway;Mercaptopurine Metabolism Pathway;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: 0.171

Intolerance Scores

• loftool: 0.526
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.06

Haploinsufficiency Scores

• pHI: 0.534
• hipred: N
• hipred_score: 0.197
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.756

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc29a2
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype

Gene ontology

• Biological process: nucleobase-containing compound metabolic process;cell population proliferation;adenine transport;guanine transport;nucleoside transport;uridine transport;hypoxanthine transport;thymine transport;neurotransmitter reuptake;nucleoside transmembrane transport
• Cellular component: nucleolus;plasma membrane;integral component of plasma membrane;basolateral plasma membrane;nuclear membrane;presynapse
• Molecular function: nucleoside transmembrane transporter activity