SLC25A32

solute carrier family 25 member 32, the group of Solute carrier family 25

Basic information

Region (hg38): 8:103398634-103415189

Links

ENSG00000164933 ∙ NCBI:81034 ∙ OMIM:138480 ∙ HGNC:29683 ∙ Uniprot:Q9H2D1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• exercise intolerance, riboflavin-responsive (Limited), mode of inheritance: Unknown
• exercise intolerance, riboflavin-responsive (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Exercise intolerance, riboflavin-responsive	AR	Biochemical	The condition involves recurrent exercise intolerance, and medical management (with oral riboflavin) has been described as being efficacious related to both biochemical and clinical parameters	Biochemical; Musculoskeletal	26933868

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A32 gene.

• not provided (119 variants)
• Inborn genetic diseases (18 variants)
• Exercise intolerance, riboflavin-responsive (3 variants)
• Malignant tumor of prostate (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A32 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			3	16	1	20
missense			45	3	2	50
nonsense			2			2
start loss						0
frameshift			2			2
inframe indel			2			2
splice donor/acceptor (+/-2bp)			1			1
splice region			1	5	1	7
non coding				17	27	44
Total	0	0	55	36	30

Variants in SLC25A32

This is a list of pathogenic ClinVar variants found in the SLC25A32 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-103400160-C-A			Benign (Jul 31, 2018)
8-103400246-CA-C			Benign (Jul 15, 2018)
8-103400289-A-T			Benign (Jul 31, 2018)
8-103400407-G-A		SLC25A32-related disorder	Benign/Likely benign (Jan 28, 2021)
8-103400426-T-C			Likely benign (Jan 04, 2024)
8-103400432-G-A			Likely benign (Mar 08, 2022)
8-103400445-T-C			Uncertain significance (Jan 24, 2023)
8-103400447-T-C			Likely benign (Jan 13, 2024)
8-103400457-T-G			Uncertain significance (Nov 15, 2023)
8-103400460-T-C		Exercise intolerance, riboflavin-responsive • SLC25A32-related disorder	Benign/Likely benign (Jan 29, 2024)
8-103400498-A-C		not specified	Uncertain significance (Jun 12, 2023)
8-103400500-T-A		not specified	Uncertain significance (Aug 21, 2022)
8-103400500-T-C		not specified	Uncertain significance (Dec 21, 2023)
8-103400528-TCCA-T			Uncertain significance (Jun 22, 2022)
8-103400533-C-T		SLC25A32-related disorder	Benign/Likely benign (Jan 21, 2024)
8-103400536-C-T			Uncertain significance (Mar 06, 2023)
8-103400537-G-A		SLC25A32-related disorder	Conflicting classifications of pathogenicity (Aug 28, 2023)
8-103400552-G-C			Uncertain significance (Nov 20, 2022)
8-103400556-G-GA			Benign (Aug 10, 2021)
8-103400602-C-T			Benign (Jul 31, 2018)
8-103400707-C-T			Benign (Jul 31, 2018)
8-103401273-C-T			Benign (Sep 15, 2019)
8-103401307-T-TC			Benign (Aug 14, 2018)
8-103401496-G-T			Benign/Likely benign (Jan 22, 2024)
8-103401500-T-C			Likely benign (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A32	protein_coding	protein_coding	ENST00000297578	7	16555

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.76e-9	0.260	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.369	165	179	0.922	0.00000908	2002
Missense in Polyphen		60	81.807	0.73343		915
Synonymous	-1.31	85	71.0	1.20	0.00000366	626
Loss of Function	0.589	14	16.6	0.844	7.83e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000393	0.000391
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.000161	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.000304	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transports folate across the inner membranes of mitochondria.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Metabolism;Metabolism of folate and pterines;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.518
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.335
• ghis: 0.601

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.700

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a32
• 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); embryo 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); craniofacial phenotype

Gene ontology

• Biological process: glycine metabolic process;folic acid transport;FAD transmembrane transport;folic acid metabolic process;folate import into mitochondrion
• Cellular component: mitochondrion;mitochondrial inner membrane;integral component of membrane
• Molecular function: folic acid transmembrane transporter activity;FAD transmembrane transporter activity