SLC25A42

solute carrier family 25 member 42, the group of Solute carrier family 25

Basic information

Region (hg38): 19:19063994-19113030

Links

ENSG00000181035 ∙ NCBI:284439 ∙ OMIM:610823 ∙ HGNC:28380 ∙ Uniprot:Q86VD7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression (Moderate), mode of inheritance: AR
• metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression (Strong), mode of inheritance: AR
• metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression	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; Musculoskeletal; Neurologic; Renal	26541337; 29327420; 29923093

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A42 gene.

• not_provided (153 variants)
• Inborn_genetic_diseases (33 variants)
• SLC25A42-related_disorder (3 variants)
• Metabolic_crises,_recurrent,_with_variable_encephalomyopathic_features_and_neurologic_regression (2 variants)
• Inborn_mitochondrial_myopathy (2 variants)
• SLC25A42-related_mitochondrial_encephalomyopathy (1 variants)
• SLC25A42-related_mitochondrial_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A42 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000178526.5. 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			2	53	2	57
missense		1	64	1	1	67
nonsense		1	1			2
start loss						0
frameshift		1	2			3
splice donor/acceptor (+/-2bp)	1		1			2
Total	1	3	70	54	3

Highest pathogenic variant AF is 0.00000344876

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A42	protein_coding	protein_coding	ENST00000318596	7	48890

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.489	0.510	125735	0	11	125746	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.10	120	205	0.586	0.0000131	2003
Missense in Polyphen		42	98.963	0.4244		963
Synonymous	-0.0695	92	91.2	1.01	0.00000595	691
Loss of Function	2.82	3	14.7	0.204	7.92e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000532	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000671	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial carrier mediating the transport of coenzyme A (CoA) in mitochondria in exchange for intramitochondrial (deoxy)adenine nucleotides and adenosine 3',5'- diphosphate. {ECO:0000269|PubMed:19429682}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.428
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.263
• hipred: Y
• hipred_score: 0.662
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.944

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a42

Zebrafish Information Network

• Gene name: slc25a42
• Affected structure: skeletal muscle
• Phenotype tag: abnormal
• Phenotype quality: swollen

Gene ontology

• Biological process: ADP transport;ATP transport;coenzyme A transmembrane transport;AMP transport
• Cellular component: nucleus;mitochondrion;mitochondrial inner membrane;integral component of membrane
• Molecular function: ATP transmembrane transporter activity;ADP transmembrane transporter activity;coenzyme A transmembrane transporter activity;adenosine-diphosphatase activity;AMP transmembrane transporter activity