SLC25A38

solute carrier family 25 member 38, the group of Solute carrier family 25

Basic information

Region (hg38): 3:39383370-39397351

Links

ENSG00000144659 ∙ NCBI:54977 ∙ OMIM:610819 ∙ HGNC:26054 ∙ Uniprot:Q96DW6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• sideroblastic anemia 2 (Definitive), mode of inheritance: AR
• sideroblastic anemia 2 (Strong), mode of inheritance: AR
• sideroblastic anemia 2 (Definitive), mode of inheritance: AR
• sideroblastic anemia 2 (Strong), mode of inheritance: AR
• autosomal recessive sideroblastic anemia (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Anemia, sideroblastic 2, pyridoxine-refractory	AR	Hematologic	Individuals may have chronic, transfusion-dependent anemia refractory to pyridoxine, and diagnosis may allow early transfusion-based treatment	Hematologic	19412178; 21393332

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A38 gene.

• not_provided (119 variants)
• Sideroblastic_anemia_2 (79 variants)
• Inborn_genetic_diseases (39 variants)
• not_specified (7 variants)
• X-linked_sideroblastic_anemia_1 (7 variants)
• SLC25A38-related_disorder (5 variants)
• Refractory_anemia_with_ringed_sideroblasts (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A38 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017875.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous	1		3	31		35
missense	15	7	64	6		92
nonsense	9	1				10
start loss			1			1
frameshift	16	5				21
splice donor/acceptor (+/-2bp)	7	2	1			10
Total	48	15	69	37	0

Highest pathogenic variant AF is 0.00027327586

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A38	protein_coding	protein_coding	ENST00000273158	7	14004

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000943	0.794	125671	0	77	125748	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.263	162	172	0.943	0.0000104	1951
Missense in Polyphen		63	73.511	0.85701		816
Synonymous	0.537	60	65.5	0.916	0.00000392	646
Loss of Function	1.26	10	15.3	0.653	9.04e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000691	0.000691
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000457	0.000457
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: 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-aminolevulinate (ALA) in the mitochondrial matrix. Required during erythropoiesis. {ECO:0000255|HAMAP-Rule:MF_03064, ECO:0000269|PubMed:19412178, ECO:0000269|PubMed:27476175}.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.653
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.214
• hipred: N
• hipred_score: 0.351
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.847

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a38
• Phenotype: growth/size/body region phenotype

Gene ontology

• Biological process: heme biosynthetic process;erythrocyte differentiation;glycine import into mitochondrion
• Cellular component: mitochondrion;mitochondrial inner membrane;integral component of membrane
• Molecular function: glycine transmembrane transporter activity