SLC29A4

solute carrier family 29 member 4, the group of Solute carrier family 29

Basic information

Region (hg38): 7:5274369-5306912

Links

ENSG00000164638 ∙ NCBI:222962 ∙ OMIM:609149 ∙ HGNC:23097 ∙ Uniprot:Q7RTT9 ∙ 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 SLC29A4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC29A4 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				3	3	6
missense			66	4	2	72
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	67	7	5

Variants in SLC29A4

This is a list of pathogenic ClinVar variants found in the SLC29A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-5287856-G-A		not specified	Uncertain significance (Feb 11, 2025)
7-5287886-A-C			Benign (Dec 31, 2019)
7-5287900-C-T		SLC29A4-related disorder	Likely benign (Jul 01, 2019)
7-5287901-G-A		not specified	Uncertain significance (Dec 20, 2023)
7-5287902-A-G		SLC29A4-related disorder	Benign (Feb 21, 2019)
7-5287923-C-T		not specified	Uncertain significance (Nov 14, 2024)
7-5287926-C-T		not specified	Uncertain significance (Jun 07, 2024)
7-5287927-G-A		SLC29A4-related disorder	Likely benign (Nov 21, 2019)
7-5287928-G-GAGGCGGCTC			Uncertain significance (Nov 27, 2017)
7-5287932-C-T		not specified	Uncertain significance (Feb 23, 2023)
7-5287959-G-T		not specified	Uncertain significance (Jan 17, 2025)
7-5287970-G-C		not specified	Uncertain significance (Oct 16, 2024)
7-5290737-G-A		not specified	Uncertain significance (Sep 09, 2021)
7-5290752-G-A		not specified	Uncertain significance (Jan 09, 2025)
7-5290780-C-T		not specified	Uncertain significance (May 22, 2023)
7-5290792-C-A		not specified	Uncertain significance (Aug 04, 2023)
7-5290797-G-A		not specified	Uncertain significance (Feb 24, 2022)
7-5291127-C-T		not specified	Uncertain significance (Jun 07, 2023)
7-5291141-G-A		not specified	Uncertain significance (Jun 26, 2024)
7-5291183-C-G		not specified	Uncertain significance (Jun 10, 2024)
7-5291183-C-T		not specified	Uncertain significance (Apr 19, 2023)
7-5291195-G-A		not specified	Uncertain significance (Dec 23, 2024)
7-5291233-C-G		SLC29A4-related disorder	Likely benign (Feb 01, 2023)
7-5291716-C-T		not specified	Uncertain significance (Dec 14, 2023)
7-5291725-A-G		not specified	Uncertain significance (Feb 01, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC29A4	protein_coding	protein_coding	ENST00000396872	10	32502

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000114	0.951	125675	0	68	125743	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.00	420	366	1.15	0.0000250	3392
Missense in Polyphen		112	114.49	0.97825		1099
Synonymous	-7.15	292	172	1.69	0.0000134	1130
Loss of Function	1.82	11	19.7	0.557	9.06e-7	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000180	0.000178
Ashkenazi Jewish	0.000324	0.000298
East Asian	0.000110	0.000109
Finnish	0.000169	0.000139
European (Non-Finnish)	0.000402	0.000387
Middle Eastern	0.000110	0.000109
South Asian	0.000262	0.000261
Other	0.000517	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a polyspecific organic cation transporter, efficiently transporting many organic cations such as monoamine neurotransmitters 1-methyl-4-phenylpyridinium and biogenic amines including serotonin, dopamine, norepinephrine and epinephrine. May play a role in regulating central nervous system homeostasis of monoamine neurotransmitters. May be involved in luminal transport of organic cations in the kidney and seems to use luminal proton gradient to drive organic cation reabsorption. Does not seem to transport nucleoside and nucleoside analogs such as uridine, cytidine, thymidine, adenosine, inosine, guanosine, and azidothymidine. In (PubMed:16873718) adenosine is efficiently transported but in a fashion highly sensitive to extracellular pH, with maximal activity in the pH range 5.5 to 6.5. Glu-206 is essential for the cation selectivity and may function as the charge sensor for cationic substrates. Transport is chloride and sodium-independent but appears to be sensitive to changes in membrane potential. Weakly inhibited by the classical inhibitors of equilibrative nucleoside transport, dipyridamole, dilazep, and nitrobenzylthioinosine. May play a role in the regulation of extracellular adenosine concentrations in cardiac tissues, in particular during ischemia. {ECO:0000269|PubMed:15448143, ECO:0000269|PubMed:16873718, ECO:0000269|PubMed:17018840, ECO:0000269|PubMed:17121826}.
• Pathway: Metformin Pathway, Pharmacokinetics;Tyrosine metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.566
• rvis_EVS: -0.99
• rvis_percentile_EVS: 8.64

Haploinsufficiency Scores

• pHI: 0.225
• hipred: N
• hipred_score: 0.390
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.254

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc29a4
• 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)

Gene ontology

• Biological process: monoamine transport;nucleoside transmembrane transport
• Cellular component: plasma membrane;integral component of membrane;apical plasma membrane
• Molecular function: nucleoside transmembrane transporter activity;monoamine transmembrane transporter activity