SLC25A26

solute carrier family 25 member 26, the group of Solute carrier family 25

Basic information

Region (hg38): 3:66133609-66388116

Links

ENSG00000144741 ∙ NCBI:115286 ∙ OMIM:611037 ∙ HGNC:20661 ∙ Uniprot:Q70HW3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation deficiency 28 (Strong), mode of inheritance: AR
• combined oxidative phosphorylation deficiency 28 (Supportive), mode of inheritance: AR
• combined oxidative phosphorylation deficiency 28 (Strong), mode of inheritance: AR
• mitochondrial disease (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 28	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Cardiovascular; Neurologic	26522469

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A26 gene.

• not provided (118 variants)
• Inborn genetic diseases (63 variants)
• Combined oxidative phosphorylation deficiency 28 (8 variants)
• not specified (4 variants)
• LRIG1-related condition (1 variants)
• Hypokalemic periodic paralysis, type 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A26 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				8	2	10
missense			25	4	4	33
nonsense	1					1
start loss				1		1
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region			2	7	1	10
non coding			39	31	56	126
Total	1	2	66	44	62

Highest pathogenic variant AF is 0.0000132

Variants in SLC25A26

This is a list of pathogenic ClinVar variants found in the SLC25A26 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-66220525-G-C			Benign (Jun 14, 2018)
3-66220535-C-T			Benign (Jun 14, 2018)
3-66220543-G-A			Benign (Jun 14, 2018)
3-66220743-T-A			Benign (Jun 14, 2018)
3-66220821-C-G			Benign (Jun 14, 2018)
3-66220872-C-A			Benign (Sep 18, 2018)
3-66220897-C-G			Likely benign (Aug 14, 2018)
3-66220945-G-T			Likely benign (Jul 27, 2018)
3-66221047-C-T			Likely benign (Jun 16, 2018)
3-66221082-G-A		not specified	Uncertain significance (Oct 20, 2023)
3-66221098-G-T		Inborn genetic diseases	Uncertain significance (Aug 12, 2022)
3-66221127-G-A			Likely benign (Aug 27, 2020)
3-66221128-G-A		Combined oxidative phosphorylation deficiency 28	Likely pathogenic (Oct 26, 2022)
3-66221164-C-T			Benign (Jun 14, 2018)
3-66221175-C-T			Likely benign (Jan 23, 2020)
3-66221177-T-C			Benign (Jun 16, 2018)
3-66221191-C-C			Benign (Jun 14, 2018)
3-66221319-C-T			Likely benign (Jun 29, 2019)
3-66221358-G-G			Benign (Jun 14, 2018)
3-66236234-G-A			Benign (Jun 14, 2018)
3-66236253-G-A			Benign (Jun 16, 2018)
3-66236273-T-G			Likely benign (Jul 26, 2019)
3-66236324-A-G			Likely benign (Aug 17, 2018)
3-66236384-G-A			Benign (Jun 14, 2018)
3-66236407-G-T			Benign (Jun 14, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A26	protein_coding	protein_coding	ENST00000354883	10	319256

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.58e-7	0.507	125553	0	40	125593	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.391	144	131	1.10	0.00000635	1711
Missense in Polyphen		41	39.812	1.0298		499
Synonymous	0.511	45	49.6	0.908	0.00000243	558
Loss of Function	0.870	12	15.7	0.763	7.96e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000390	0.000386
Ashkenazi Jewish	0.00	0.00
East Asian	0.000222	0.000218
Finnish	0.00	0.00
European (Non-Finnish)	0.000192	0.000176
Middle Eastern	0.000222	0.000218
South Asian	0.000100	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial solute carriers shuttle metabolites, nucleotides, and cofactors through the mitochondrial inner membrane. Specifically mediates the transport of S- adenosylmethionine (SAM) into the mitochondria. {ECO:0000269|PubMed:14674884, ECO:0000269|PubMed:26522469}.
• Pathway: Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Methionine and cysteine metabolism (Consensus)

Recessive Scores

• pRec: 0.0908

Intolerance Scores

• loftool: 0.693
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.255
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0167

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a26
• Phenotype: growth/size/body region 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); embryo phenotype

Gene ontology

• Biological process: ion transport;S-adenosyl-L-methionine transport;S-adenosyl-L-methionine transmembrane transport
• Cellular component: mitochondrion;mitochondrial inner membrane;integral component of membrane
• Molecular function: S-adenosyl-L-methionine transmembrane transporter activity