SLC29A3

solute carrier family 29 member 3, the group of Solute carrier family 29

Basic information

Region (hg38): 10:71319259-71381423

Links

ENSG00000198246 ∙ NCBI:55315 ∙ OMIM:612373 ∙ HGNC:23096 ∙ Uniprot:Q9BZD2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• H syndrome (Strong), mode of inheritance: AR
• dysosteosclerosis (Supportive), mode of inheritance: AR
• H syndrome (Supportive), mode of inheritance: AR
• H syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Histiocytosis-lymphadenopathy plus syndrome	AR	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Dermatologic; Endocrine	Lipogranulomatous infiltration has been reported as benefiting from surgical interventions, radiotherapy, and medical treatment (eg, with cylophosphamide, prednisolone); Hormonal insufficiency, including hypogonadotropic hypogonadism, hypothyroidism, and growth hormone deficiency, may benefit from medical treatment; Individuals may manifest with early-onset hearing loss, and early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Dermatologic; Endocrine; Gastrointestinal; Musculoskeletal	16118898; 16631937; 16650224; 16155931; 16155931; 18940313; 19336477; 19175903; 19889517; 20140240; 20199414; 20199539; 20399510; 20619369; 21178579; 21888995; 22238637; 22356918; 22653152; 22875837; 22989030; 23058913; 23406517; 23530176; 23623699

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC29A3 gene.

• H syndrome (24 variants)
• not provided (5 variants)
• SLC29A3-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC29A3 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			4	109	9	122
missense	4	4	200	5	7	220
nonsense	2	3	2			7
start loss						0
frameshift	16		1			17
inframe indel			6			6
splice donor/acceptor (+/-2bp)	3	3				6
splice region		1	3	9	3	16
non coding			16	31	18	65
Total	25	10	229	145	34

Highest pathogenic variant AF is 0.0000591

Variants in SLC29A3

This is a list of pathogenic ClinVar variants found in the SLC29A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-71319279-G-C		H syndrome	Uncertain significance (Jan 13, 2018)
10-71319287-C-T		H syndrome	Uncertain significance (Jan 13, 2018)
10-71319303-C-T		H syndrome	Benign (Jan 13, 2018)
10-71319312-T-G		H syndrome	Likely pathogenic (Nov 08, 2022)
10-71319318-C-T		H syndrome	Likely benign (Dec 11, 2023)
10-71319324-G-C		H syndrome	Likely benign (Aug 30, 2023)
10-71319390-G-A		not specified	Benign (Jan 24, 2024)
10-71319472-T-C			Benign (Nov 12, 2018)
10-71319545-C-G			Benign (Jun 19, 2021)
10-71322739-C-T		H syndrome	Benign (Jan 21, 2024)
10-71322744-T-C		H syndrome	Likely benign (May 18, 2021)
10-71322750-C-T		H syndrome	Likely benign (Jun 18, 2021)
10-71322752-A-G		H syndrome	Likely pathogenic (Oct 21, 2022)
10-71322756-T-A		H syndrome	Likely pathogenic (Jun 10, 2023)
10-71322759-C-T		H syndrome	Uncertain significance (Jul 06, 2022)
10-71322760-C-T		H syndrome	Likely benign (Nov 18, 2023)
10-71322761-G-A		H syndrome	Uncertain significance (Apr 12, 2022)
10-71322764-G-A		H syndrome	Uncertain significance (Dec 11, 2020)
10-71322772-G-A		H syndrome	Likely benign (Oct 11, 2023)
10-71322775-C-A		H syndrome • Inborn genetic diseases	Uncertain significance (Jul 13, 2022)
10-71322775-C-T		H syndrome	Likely benign (Jan 29, 2024)
10-71322776-G-A		H syndrome • Inborn genetic diseases	Uncertain significance (Dec 19, 2023)
10-71322785-C-G		H syndrome	Uncertain significance (Jun 22, 2021)
10-71322794-A-G		H syndrome	Uncertain significance (Dec 11, 2023)
10-71322805-CA-TG		H syndrome	Likely benign (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC29A3	protein_coding	protein_coding	ENST00000373189	6	44128

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.29e-7	0.372	125694	1	53	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.477	292	270	1.08	0.0000173	3055
Missense in Polyphen		103	90.015	1.1442		1056
Synonymous	-1.49	145	124	1.17	0.00000894	1046
Loss of Function	0.652	12	14.7	0.816	7.28e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000713	0.000713
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.000110	0.000109
South Asian	0.000523	0.000490
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates both influx and efflux of nucleosides across the membrane (equilibrative transporter). Mediates transport of adenine, adenosine and uridine, as well as several nucleoside analog drugs, such as anticancer and antiviral agents, including cladribine, cordycepin, tubercidin and AZT. Does not transport hypoxanthine. {ECO:0000269|PubMed:15701636}.
• 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: 0.135

Intolerance Scores

• loftool: 0.595
• rvis_EVS: 0.43
• rvis_percentile_EVS: 77.29

Haploinsufficiency Scores

• pHI: 0.260
• hipred: N
• hipred_score: 0.219
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.468

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Slc29a3
• Phenotype: cellular phenotype; neoplasm; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype

Gene ontology

• Biological process: nucleoside transmembrane transport
• Cellular component: lysosomal membrane;Golgi apparatus;integral component of membrane;late endosome membrane;intracellular membrane-bounded organelle
• Molecular function: nucleoside transmembrane transporter activity;protein binding