SLC25A19 (solute carrier family 25 member 19)

Gene

• Entrez ID: 60386
• Gene name: Solute carrier family 25 member 19
• Gene symbol: SLC25A19
• Synonyms (NCBI Gene): DNC, MCPHA, MTPPT, MUP1, THMD3, THMD4, TPC
• Chromosome: 17
• Chromosome location: 17q25.1
• Summary: This gene encodes a mitochondrial protein that is a member of the solute carrier family. Although this protein was initially thought to be the mitochondrial deoxynucleotide carrier involved in the uptake of deoxynucleotides into the matrix of the mitochon

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs119473030	C>G	Pathogenic	Coding sequence variant, intron variant, missense variant
rs143765189	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, synonymous variant
rs147904037	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Intron variant, synonymous variant, coding sequence variant
rs148474667	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Intron variant, synonymous variant, coding sequence variant
rs387906944	C>T	Pathogenic	Coding sequence variant, missense variant
rs554218525	G>A,T	Likely-pathogenic	Missense variant, intron variant, coding sequence variant
rs759157320	C>T	Likely-pathogenic	Coding sequence variant, missense variant, intron variant
rs769187207	C>A,G	Pathogenic	Intron variant, missense variant, coding sequence variant
rs1175745274	T>C,G	Likely-pathogenic	Missense variant, coding sequence variant, synonymous variant, 5 prime UTR variant
rs1208990609	C>T	Pathogenic	Coding sequence variant, intron variant, missense variant
rs1555603796	G>T	Pathogenic	Coding sequence variant, missense variant
rs1555604541	G>A	Pathogenic	5 prime UTR variant, coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT020598	hsa-miR-155-5p	Proteomics	18668040
MIRT023578	hsa-miR-1-3p	Proteomics	18668040
MIRT032289	hsa-let-7b-5p	Proteomics	18668040
MIRT439616	hsa-miR-543	HITS-CLIP	24374217
MIRT439616	hsa-miR-543	HITS-CLIP	24374217
MIRT1355574	hsa-miR-1	CLIP-seq
MIRT1355575	hsa-miR-206	CLIP-seq
MIRT1355576	hsa-miR-4796-5p	CLIP-seq
MIRT1355577	hsa-miR-613	CLIP-seq
MIRT2329881	hsa-miR-4656	CLIP-seq
MIRT2624075	hsa-miR-205	CLIP-seq
MIRT2624076	hsa-miR-3667-3p	CLIP-seq
MIRT2624077	hsa-miR-4433	CLIP-seq
MIRT2624078	hsa-miR-4459	CLIP-seq
MIRT2624079	hsa-miR-4695-5p	CLIP-seq
MIRT2624080	hsa-miR-4768-3p	CLIP-seq
MIRT2624081	hsa-miR-485-5p	CLIP-seq
MIRT2690976	hsa-miR-15a	CLIP-seq
MIRT2690977	hsa-miR-15b	CLIP-seq
MIRT2690978	hsa-miR-16	CLIP-seq
MIRT2690979	hsa-miR-195	CLIP-seq
MIRT2690980	hsa-miR-1976	CLIP-seq
MIRT2690981	hsa-miR-3130-3p	CLIP-seq
MIRT2690982	hsa-miR-3189-5p	CLIP-seq
MIRT2690983	hsa-miR-424	CLIP-seq
MIRT2690984	hsa-miR-4323	CLIP-seq
MIRT2690985	hsa-miR-4512	CLIP-seq
MIRT2690986	hsa-miR-4687-5p	CLIP-seq
MIRT2690987	hsa-miR-4793-3p	CLIP-seq
MIRT2690988	hsa-miR-497	CLIP-seq
MIRT2690989	hsa-miR-518a-5p	CLIP-seq
MIRT2690990	hsa-miR-527	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005634	Component	Nucleus	HDA	21630459
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IDA	15539640, 31506564
GO:0005739	Component	Mitochondrion	IEA
GO:0005743	Component	Mitochondrial inner membrane	IBA
GO:0005743	Component	Mitochondrial inner membrane	IEA
GO:0005743	Component	Mitochondrial inner membrane	TAS
GO:0009229	Process	Thiamine diphosphate biosynthetic process	IEA
GO:0015234	Function	Thiamine transmembrane transporter activity	IBA
GO:0015297	Function	Antiporter activity	IEA
GO:0016020	Component	Membrane	IEA
GO:0030233	Function	Deoxynucleotide transmembrane transporter activity	IDA	15539640, 17035501
GO:0030233	Function	Deoxynucleotide transmembrane transporter activity	TAS	11226231
GO:0030302	Process	Deoxynucleotide transport	IDA	15539640
GO:0030302	Process	Deoxynucleotide transport	NAS	11226231
GO:0030974	Process	Thiamine pyrophosphate transmembrane transport	IBA
GO:0030974	Process	Thiamine pyrophosphate transmembrane transport	IDA	17035501
GO:0031966	Component	Mitochondrial membrane	IEA
GO:0042723	Process	Thiamine-containing compound metabolic process	IEA
GO:0042723	Process	Thiamine-containing compound metabolic process	TAS
GO:0055085	Process	Transmembrane transport	IEA
GO:0090422	Function	Thiamine pyrophosphate transmembrane transporter activity	IDA	17035501
GO:0090422	Function	Thiamine pyrophosphate transmembrane transporter activity	IEA
GO:0090422	Function	Thiamine pyrophosphate transmembrane transporter activity	TAS

Other IDs

• MIM: 606521
• HGNC: 14409
• e!Ensembl: ENSG00000125454

Protein

• UniProt ID: Q9HC21
• Protein name: Mitochondrial thiamine pyrophosphate carrier (Mitochondrial thiamine pyrophosphate transporter) (MTPPT) (Mitochondrial uncoupling protein 1) (Solute carrier family 25 member 19)
• Protein function: Mitochondrial transporter mediating uptake of thiamine diphosphate into mitochondria. It is not clear if the antiporter activity is affected by the membrane potential or by the proton electrochemical gradient. {ECO:0000269|PubMed:17035501, ECO:0
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00153	Mito_carr	12 → 111	Mitochondrial carrier protein	Family
  PF00153	Mito_carr	114 → 206	Mitochondrial carrier protein	Family
  PF00153	Mito_carr	212 → 314	Mitochondrial carrier protein	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed in all tissues examined except for placenta. Highest levels in colon, kidney, lung, testis, spleen, and brain. {ECO:0000269|PubMed:11226231}.
• Sequence:

  MVGYDPKPDGRNNTKFQVAVAGSVSGLVTRALISPFDVIKIRFQLQHERLSRSDPSAKYH
  GILQASRQILQEEGPTAFWKGHVPAQILSIGYGAVQFLSFEMLTELVHRGSVYDAREFSV
  HFVCGGLAACMATLTVHPVDVLRTRFAAQGEPKVYNTLRHAVGTMYRSEGPQVFYKGLAP
  TLIAIFPYAGLQFSCYSSLKHLYKWAIPAEGKKNENLQNLLCGSGAGVISKTLTYPLDLF
  KKRLQVGGFEHARAAFGQVRRYKGLMDCAKQVLQKEGALGFFKGLSPSLLKAALSTGFMF
  FSYEFFCNVFHCMNRTASQR

• Sequence length: 320

Pathways

Reactome:

Vitamin B1 (thiamin) metabolism

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Amish lethal microcephaly	Pathogenic; Likely pathogenic	rs119473030, rs387906944, rs554218525, rs372041843	RCV000004490 RCV001847622 RCV000853268 RCV000853269	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Progressive demyelinating neuropathy with bilateral striatal necrosis	Pathogenic; Likely pathogenic	rs1300370754, rs750590533, rs1598180323, rs181826033, rs2145724052, rs387906944, rs769187207, rs1555603796, rs1555604541, rs1175745274	RCV002264842 RCV002264843 RCV002264844 RCV002264845 RCV002264846 RCV000023554 RCV000656121 RCV000656119 RCV000656118 RCV000578249	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Hepatocellular carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEIGH SYNDROME	—	ClinGen, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROCEPHALY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROCEPHALY, AMISH TYPE	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SLC25A19-related disorder	Conflicting classifications of pathogenicity; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYSTEMIC LUPUS ERYTHEMATOSUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
THIAMINE METABOLISM DYSFUNCTION SYNDROME 4	—	CTD, HPO CTD, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenomatous Polyposis Coli	Multiple polyposis syndrome	BEFREE	30482542		★☆☆☆☆ Found in Text Mining only
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Amish lethal microcephaly	Lethal Microcephaly	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Amish lethal microcephaly	Amish lethal microcephaly	Pubtator	31506564, 34587972	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Brain Diseases	Brain disease	Pubtator	34587972	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	27353380, 29990474		★☆☆☆☆ Found in Text Mining only
Cerebellar Hypoplasia	Cerebellar Hypoplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cleft Soft Palate	Cleft Soft Palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	29703930	Associate	★☆☆☆☆ Found in Text Mining only
Congenital clubfoot	Congenital Clubfoot	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cushing Syndrome	Cushing`s Syndrome	BEFREE	28834902		★☆☆☆☆ Found in Text Mining only
Defect of skull ossification	Defect Of Skull Ossification	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	29227974		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	20831945		★☆☆☆☆ Found in Text Mining only
Giant Cell Arteritis	Giant Cell Arteritis	BEFREE	30554380		★☆☆☆☆ Found in Text Mining only
Hyperglycemia	Hyperglycemia	BEFREE	20831945		★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	BEFREE	30554380		★☆☆☆☆ Found in Text Mining only
Leigh Disease	Leigh Syndrome	BEFREE	28706281		★☆☆☆☆ Found in Text Mining only
Leigh Disease	Leigh syndrome	Pubtator	36093993	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	29975953		★☆☆☆☆ Found in Text Mining only
Lissencephaly	Lissencephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	27353380, 29990474		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28393212		★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic Diseases	BEFREE	30687113		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	LHGDN	12185364		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Microcephaly	BEFREE	19798730, 28706281		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Microcephaly	Pubtator	31506564	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Microcephaly	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROCEPHALY, AMISH TYPE (disorder)	Microcephaly	BEFREE	12185364, 31506564		★☆☆☆☆ Found in Text Mining only
MICROCEPHALY, AMISH TYPE (disorder)	Microcephaly	GENOMICS_ENGLAND_DG	12185364, 17035501, 19798730, 27604308		★☆☆☆☆ Found in Text Mining only
MICROCEPHALY, AMISH TYPE (disorder)	Microcephaly	UNIPROT_DG	12185364		★☆☆☆☆ Found in Text Mining only
MICROCEPHALY, AMISH TYPE (disorder)	Microcephaly	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
MICROCEPHALY, AMISH TYPE (disorder)	Microcephaly	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	26316591, 31801972		★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	28058510, 28706281		★☆☆☆☆ Found in Text Mining only
Neuropathy	Neuropathy	BEFREE	19798730		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	12565902, 28120848, 30687113		★☆☆☆☆ Found in Text Mining only
Obesity Morbid	Obesity	Pubtator	32734695	Associate	★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Papilloma Choroid Plexus	Choroid plexus papilloma	Pubtator	29703930	Associate	★☆☆☆☆ Found in Text Mining only
Partial agenesis of corpus callosum	Partial Agenesis Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Peripheral axonal neuropathy	Peripheral axonal neuropathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polyneuropathies	Polyneuropathy	Pubtator	34587972	Associate	★☆☆☆☆ Found in Text Mining only
Polyneuropathy	Polyneuropathy	BEFREE	19798730, 31295743		★☆☆☆☆ Found in Text Mining only
Polyneuropathy	Polyneuropathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Progressive polyneuropathy with bilateral striatal necrosis	Progressive polyneuropathy with bilateral striatal necrosis	GENOMICS_ENGLAND_DG	17035501, 19798730, 27604308		★☆☆☆☆ Found in Text Mining only
Progressive polyneuropathy with bilateral striatal necrosis	Progressive polyneuropathy with bilateral striatal necrosis	ORPHANET_DG	19798730		★☆☆☆☆ Found in Text Mining only
Progressive polyneuropathy with bilateral striatal necrosis	Progressive polyneuropathy with bilateral striatal necrosis	UNIPROT_DG	19798730		★☆☆☆☆ Found in Text Mining only
Progressive polyneuropathy with bilateral striatal necrosis	Progressive polyneuropathy with bilateral striatal necrosis	Orphanet			★☆☆☆☆ Found in Text Mining only
Progressive polyneuropathy with bilateral striatal necrosis	Progressive polyneuropathy with bilateral striatal necrosis	BEFREE	31506564		★☆☆☆☆ Found in Text Mining only
Progressive polyneuropathy with bilateral striatal necrosis	Progressive polyneuropathy with bilateral striatal necrosis	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Progressive polyneuropathy with bilateral striatal necrosis	Progressive polyneuropathy with bilateral striatal necrosis	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Spina Bifida	Spina Bifida	HPO_DG			★☆☆☆☆ Found in Text Mining only
Tonic - clonic seizures	Seizure	HPO_DG			★☆☆☆☆ Found in Text Mining only