Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	54977
Gene name	Solute carrier family 25 member 38
Gene symbol	SLC25A38
Synonyms (NCBI Gene)	SIDBA2
Chromosome	3
Chromosome location	3p22.1
Summary	This gene is a member of the mitochondrial carrier family. The encoded protein is required during erythropoiesis and is important for the biosynthesis of heme. Mutations in this gene are the cause of autosomal congenital sideroblastic anemia (anemia, side

Show/Hide all (9)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121918330	C>T	Pathogenic	Stop gained, coding sequence variant
rs121918331	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs121918332	A>T	Pathogenic	Stop gained, intron variant, coding sequence variant
rs146864395	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant
rs866266558	C>T	Pathogenic	Stop gained, coding sequence variant
rs869312029	G>A	Pathogenic	Splice acceptor variant
rs869320719	CT>-	Pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant
rs1233124208	A>C,G	Pathogenic	Splice acceptor variant
rs1575247302	->T	Likely-pathogenic	Coding sequence variant, frameshift variant, intron variant

129

Show/Hide all (129)

miRTarBase ID	miRNA	Experiments	Reference
MIRT051268	hsa-miR-16-5p	CLASH	23622248
MIRT049071	hsa-miR-92a-3p	CLASH	23622248
MIRT047969	hsa-miR-30c-5p	CLASH	23622248
MIRT1356645	hsa-miR-101	CLIP-seq
MIRT1356646	hsa-miR-1303	CLIP-seq
MIRT1356647	hsa-miR-142-5p	CLIP-seq
MIRT1356648	hsa-miR-146a	CLIP-seq
MIRT1356649	hsa-miR-146b-5p	CLIP-seq
MIRT1356650	hsa-miR-181a	CLIP-seq
MIRT1356651	hsa-miR-181b	CLIP-seq
MIRT1356652	hsa-miR-181c	CLIP-seq
MIRT1356653	hsa-miR-181d	CLIP-seq
MIRT1356654	hsa-miR-186	CLIP-seq
MIRT1356655	hsa-miR-217	CLIP-seq
MIRT1356656	hsa-miR-298	CLIP-seq
MIRT1356657	hsa-miR-3117-3p	CLIP-seq
MIRT1356658	hsa-miR-3133	CLIP-seq
MIRT1356659	hsa-miR-3154	CLIP-seq
MIRT1356660	hsa-miR-3158-5p	CLIP-seq
MIRT1356661	hsa-miR-3169	CLIP-seq
MIRT1356662	hsa-miR-3975	CLIP-seq
MIRT1356663	hsa-miR-4257	CLIP-seq
MIRT1356664	hsa-miR-4262	CLIP-seq
MIRT1356665	hsa-miR-4326	CLIP-seq
MIRT1356666	hsa-miR-4418	CLIP-seq
MIRT1356667	hsa-miR-4464	CLIP-seq
MIRT1356668	hsa-miR-4748	CLIP-seq
MIRT1356669	hsa-miR-4759	CLIP-seq
MIRT1356670	hsa-miR-4761-3p	CLIP-seq
MIRT1356671	hsa-miR-509-3-5p	CLIP-seq
MIRT1356672	hsa-miR-509-5p	CLIP-seq
MIRT1356673	hsa-miR-543	CLIP-seq
MIRT1356674	hsa-miR-550b	CLIP-seq
MIRT1356675	hsa-miR-561	CLIP-seq
MIRT1356676	hsa-miR-589	CLIP-seq
MIRT1356677	hsa-miR-877	CLIP-seq
MIRT2105663	hsa-miR-1254	CLIP-seq
MIRT2105664	hsa-miR-129-3p	CLIP-seq
MIRT1356648	hsa-miR-146a	CLIP-seq
MIRT1356649	hsa-miR-146b-5p	CLIP-seq
MIRT2105665	hsa-miR-15a	CLIP-seq
MIRT2105666	hsa-miR-15b	CLIP-seq
MIRT2105667	hsa-miR-16	CLIP-seq
MIRT1356654	hsa-miR-186	CLIP-seq
MIRT2105668	hsa-miR-195	CLIP-seq
MIRT1356655	hsa-miR-217	CLIP-seq
MIRT1356656	hsa-miR-298	CLIP-seq
MIRT2105669	hsa-miR-3116	CLIP-seq
MIRT1356657	hsa-miR-3117-3p	CLIP-seq
MIRT1356658	hsa-miR-3133	CLIP-seq
MIRT1356660	hsa-miR-3158-5p	CLIP-seq
MIRT1356661	hsa-miR-3169	CLIP-seq
MIRT2105670	hsa-miR-3180-5p	CLIP-seq
MIRT2105671	hsa-miR-3653	CLIP-seq
MIRT2105672	hsa-miR-424	CLIP-seq
MIRT2105673	hsa-miR-4251	CLIP-seq
MIRT2105674	hsa-miR-4252	CLIP-seq
MIRT1356666	hsa-miR-4418	CLIP-seq
MIRT2105675	hsa-miR-4504	CLIP-seq
MIRT2105676	hsa-miR-4668-5p	CLIP-seq
MIRT2105677	hsa-miR-4727-5p	CLIP-seq
MIRT1356669	hsa-miR-4759	CLIP-seq
MIRT2105678	hsa-miR-497	CLIP-seq
MIRT1356671	hsa-miR-509-3-5p	CLIP-seq
MIRT1356672	hsa-miR-509-5p	CLIP-seq
MIRT2105679	hsa-miR-542-3p	CLIP-seq
MIRT2105680	hsa-miR-544	CLIP-seq
MIRT2105681	hsa-miR-548an	CLIP-seq
MIRT2105682	hsa-miR-549	CLIP-seq
MIRT1356674	hsa-miR-550b	CLIP-seq
MIRT2105683	hsa-miR-570	CLIP-seq
MIRT1356676	hsa-miR-589	CLIP-seq
MIRT2105684	hsa-miR-595	CLIP-seq
MIRT2105685	hsa-miR-661	CLIP-seq
MIRT2330190	hsa-miR-1253	CLIP-seq
MIRT2330191	hsa-miR-3921	CLIP-seq
MIRT2330192	hsa-miR-3925-3p	CLIP-seq
MIRT2105673	hsa-miR-4251	CLIP-seq
MIRT2330193	hsa-miR-4329	CLIP-seq
MIRT2330194	hsa-miR-4653-5p	CLIP-seq
MIRT2330195	hsa-miR-515-5p	CLIP-seq
MIRT2330196	hsa-miR-520a-5p	CLIP-seq
MIRT2330197	hsa-miR-525-5p	CLIP-seq
MIRT2330198	hsa-miR-766	CLIP-seq
MIRT2105663	hsa-miR-1254	CLIP-seq
MIRT2624234	hsa-miR-1270	CLIP-seq
MIRT2624235	hsa-miR-1343	CLIP-seq
MIRT2624236	hsa-miR-1976	CLIP-seq
MIRT2624237	hsa-miR-219-2-3p	CLIP-seq
MIRT2624238	hsa-miR-2964a-3p	CLIP-seq
MIRT2105669	hsa-miR-3116	CLIP-seq
MIRT2624239	hsa-miR-3153	CLIP-seq
MIRT2105670	hsa-miR-3180-5p	CLIP-seq
MIRT2624240	hsa-miR-3591-3p	CLIP-seq
MIRT2624241	hsa-miR-3691-3p	CLIP-seq
MIRT2624242	hsa-miR-3929	CLIP-seq
MIRT2624243	hsa-miR-3936	CLIP-seq
MIRT2624244	hsa-miR-4279	CLIP-seq
MIRT2624245	hsa-miR-4419b	CLIP-seq
MIRT2624246	hsa-miR-4450	CLIP-seq
MIRT2624247	hsa-miR-4478	CLIP-seq
MIRT2624248	hsa-miR-4493	CLIP-seq
MIRT2624249	hsa-miR-4531	CLIP-seq
MIRT2624250	hsa-miR-4646-5p	CLIP-seq
MIRT2105676	hsa-miR-4668-5p	CLIP-seq
MIRT2624251	hsa-miR-4683	CLIP-seq
MIRT2624252	hsa-miR-4724-5p	CLIP-seq
MIRT2105677	hsa-miR-4727-5p	CLIP-seq
MIRT2624253	hsa-miR-532-5p	CLIP-seq
MIRT2105680	hsa-miR-544	CLIP-seq
MIRT2105681	hsa-miR-548an	CLIP-seq
MIRT2624254	hsa-miR-562	CLIP-seq
MIRT2624255	hsa-miR-620	CLIP-seq
MIRT2624256	hsa-miR-648	CLIP-seq
MIRT2105685	hsa-miR-661	CLIP-seq
MIRT2624235	hsa-miR-1343	CLIP-seq
MIRT2624236	hsa-miR-1976	CLIP-seq
MIRT2624237	hsa-miR-219-2-3p	CLIP-seq
MIRT2624238	hsa-miR-2964a-3p	CLIP-seq
MIRT2624239	hsa-miR-3153	CLIP-seq
MIRT2624240	hsa-miR-3591-3p	CLIP-seq
MIRT2624241	hsa-miR-3691-3p	CLIP-seq
MIRT2691021	hsa-miR-4330	CLIP-seq
MIRT2624250	hsa-miR-4646-5p	CLIP-seq
MIRT2105676	hsa-miR-4668-5p	CLIP-seq
MIRT2624253	hsa-miR-532-5p	CLIP-seq
MIRT2624254	hsa-miR-562	CLIP-seq
MIRT2624256	hsa-miR-648	CLIP-seq
MIRT2691022	hsa-miR-759	CLIP-seq

Show/Hide all (15)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IEA
GO:0005743	Component	Mitochondrial inner membrane	IEA
GO:0005743	Component	Mitochondrial inner membrane	ISS
GO:0006783	Process	Heme biosynthetic process	TAS	19412178
GO:0015187	Function	Glycine transmembrane transporter activity	IBA
GO:0015187	Function	Glycine transmembrane transporter activity	IEA
GO:0015187	Function	Glycine transmembrane transporter activity	IMP	27476175
GO:0016020	Component	Membrane	IEA
GO:0030218	Process	Erythrocyte differentiation	IEA
GO:0030218	Process	Erythrocyte differentiation	IMP	19412178
GO:1904983	Process	Glycine import into mitochondrion	IBA
GO:1904983	Process	Glycine import into mitochondrion	IEA
GO:1904983	Process	Glycine import into mitochondrion	IMP	27476175

MIM	HGNC	e!Ensembl
610819	26054	ENSG00000144659

Q96DW6

Protein name

Mitochondrial glycine transporter (Appoptosin) (Mitochondrial glycine transporter GlyC) (Solute carrier family 25 member 38)

Protein function

Mitochondrial glycine transporter that imports glycine into the mitochondrial matrix. Plays an important role in providing glycine for the first enzymatic step in heme biosynthesis, the condensation of glycine with succinyl-CoA to produce 5-amin

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00153	Mito_carr	24 → 119	Mitochondrial carrier protein	Family
PF00153	Mito_carr	119 → 210	Mitochondrial carrier protein	Family
PF00153	Mito_carr	214 → 304	Mitochondrial carrier protein	Family

Tissue specificity

TISSUE SPECIFICITY: Preferentially expressed in erythroid cells. {ECO:0000269|PubMed:19412178}.

Sequence

MIQNSRPSLLQPQDVGDTVETLMLHPVIKAFLCGSISGTCSTLLFQPLDLLKTRLQTLQP
SDHGSRRVGMLAVLLKVVRTESLLGLWKGMSPSIVRCVPGVGIYFGTLYSLKQYFLRGHP
PTALESVMLGVGSRSVAGVCMSPITVIKTRYESGKYGYESIYAALRSIYHSEGHRGLFSG
LTATLLRDAPFSGIYLMFYNQTKNIVPHDQVDATLIPITNFSCGIFAGILASLVTQPADV
IKTHMQLYPLKFQWIGQAVTLIFKDYGLRGFFQGGIPRALRRTLMAAMAWTVYEEMMAKM
GLKS

Sequence length

304

Interactions

View interactions

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)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Sideroblastic anemia 2	Pathogenic; Likely pathogenic	rs866266558, rs2125577893, rs2125578591, rs2125578633, rs2125578710, rs2125578753, rs1198314410, rs762067787, rs2125579714, rs2125579746, rs1301033567, rs2125579866, rs2125579946, rs762562272, rs2041767822 View all (29 more)	RCV001526380 RCV001526363 RCV001526347 RCV001526377 RCV001526373 View all (42 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SLC25A38-related disorder	Likely pathogenic; Pathogenic	rs869320719, rs767156788	RCV000778696 RCV004542301	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (16)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANEMIA, SIDEROBLASTIC	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANEMIA, SIDEROBLASTIC, 2, PYRIDOXINE-REFRACTORY	—	Disgenet, HPO Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANEMIA, SIDEROBLASTIC, PYRIDOXINE-REFRACTORY, AUTOSOMAL RECESSIVE	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE SIDEROBLASTIC ANEMIA	—	Disgenet, Orphanet Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIVERTICULITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Refractory anemia with ringed sideroblasts	Benign; Uncertain significance; Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SIDEROBLASTIC ANEMIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED SIDEROBLASTIC ANEMIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-linked sideroblastic anemia 1	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (35)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Alzheimer Disease	Alzheimer disease	Pubtator	25891083	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Alzheimer disease	Pubtator	26813789	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Amyloidosis	Amyloidosis	BEFREE	23115192		★★★★★ ★☆☆☆☆ Found in Text Mining only
Anemia	Anemia	Pubtator	39519257	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Anemia Hemolytic	Hemolytic anemia	Pubtator	31338833	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Anemia hypochromic microcytic	Hypochromic microcytic anemia	Pubtator	21393332	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Anemia Refractory	Refractory anemia	Pubtator	25955609	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Anemia Sideroblastic	Sideroblastic anemia	Pubtator	21393332, 25985931, 38360212, 39519257, 39769087	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
ANEMIA, SIDEROBLASTIC, 2, PYRIDOXINE-REFRACTORY	Anemia	GENOMICS_ENGLAND_DG	19412178, 21393332		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANEMIA, SIDEROBLASTIC, 2, PYRIDOXINE-REFRACTORY	Anemia	CLINVAR_DG	19412178, 21393332, 25985931		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANEMIA, SIDEROBLASTIC, 2, PYRIDOXINE-REFRACTORY	Anemia	UNIPROT_DG	19412178		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Anemia, Sideroblastic, Pyridoxine-Refractory, Autosomal Recessive	Anemia	GENOMICS_ENGLAND_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Anemia, Sideroblastic, Pyridoxine-Refractory, Autosomal Recessive	Anemia	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autosomal recessive sideroblastic anemia	Sideroblastic Anemia	ORPHANET_DG	19412178		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autosomal recessive sideroblastic anemia	Sideroblastic Anemia	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autosomal recessive sideroblastic anemia	Sideroblastic Anemia	BEFREE	21393332, 26637696		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cockayne Syndrome	Cockayne syndrome	Pubtator	19731322	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cockayne Syndrome, Type I	Cockayne Syndrome	BEFREE	27038157, 29499877, 31338833		★★★★★ ★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	37509133	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Frontotemporal dementia	Frontotemporal dementia	BEFREE	26335643		★★★★★ ★☆☆☆☆ Found in Text Mining only
insulinoma	Insulinoma	BEFREE	29568862		★★★★★ ★☆☆☆☆ Found in Text Mining only
Iron Overload	Iron Overload	BEFREE	28772256		★★★★★ ★☆☆☆☆ Found in Text Mining only
Iron-Refractory Iron Deficiency Anemia	Anemia	BEFREE	26637696, 31338833		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	30076742		★★★★★ ★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	26335643		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neurodegenerative Disorders	Neurodegenerative Disorders	BEFREE	23115192, 31551758		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pick Disease of the Brain	Pica	BEFREE	26335643		★★★★★ ★☆☆☆☆ Found in Text Mining only
Progressive supranuclear palsy	Progressive Supranuclear Palsy	BEFREE	26335643, 31551758		★★★★★ ★☆☆☆☆ Found in Text Mining only
Refractory anemia with ringed sideroblasts	Anemia With Ringed Sideroblasts	BEFREE	25955609		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sideroblastic anemia	Sideroblastic Anemia	CTD_human_DG	19412178		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sideroblastic anemia	Sideroblastic Anemia	BEFREE	19786205, 20848343, 21393332, 27038157		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sleep Apnea, Central	Sleep Apnea	BEFREE	27038157, 29499877, 31338833		★★★★★ ★☆☆☆☆ Found in Text Mining only
Sleep Deprivation	Sleep deprivation	Pubtator	26813789	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uveal melanoma	Uveal melanoma	Pubtator	34434692	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
X-linked sideroblastic anemia	Sideroblastic Anemia, X-Linked	BEFREE	30737140		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

SLC25A38 (solute carrier family 25 member 38)