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.

not_specified (113 variants)
SLC29A4-related_disorder (18 variants)
not_provided (14 variants)

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. These statistics are base on transcript: NM_000153247.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				11 clinvar	4 clinvar	15
missense			112 clinvar	7 clinvar	3 clinvar	122
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	112	18	7

Loading clinvar variants...

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