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 (Strong), mode of inheritance: AR
• 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

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.

• Metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression (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.

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			1	39	4	44
missense		1	48	1	1	51
nonsense		1	1			2
start loss						0
frameshift		1				1
inframe indel			2			2
splice donor/acceptor (+/-2bp)	1					1
splice region			3	6		9
non coding				29	8	37
Total	1	3	52	69	13

Highest pathogenic variant AF is 0.00000661

Variants in SLC25A42

This is a list of pathogenic ClinVar variants found in the SLC25A42 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19096128-G-T			Uncertain significance (Jul 03, 2022)
19-19096150-C-T		Inborn genetic diseases	Uncertain significance (Oct 25, 2022)
19-19096151-G-A			Likely benign (Nov 20, 2023)
19-19096156-G-A		Inborn genetic diseases	Uncertain significance (Jan 23, 2023)
19-19096172-T-C			Likely benign (Feb 21, 2022)
19-19096187-C-G			Likely benign (Jun 14, 2023)
19-19096189-C-T		Inborn genetic diseases	Uncertain significance (Jul 13, 2022)
19-19096190-G-A			Likely benign (Feb 10, 2022)
19-19096193-C-A			Likely benign (Aug 16, 2022)
19-19096193-C-T			Likely benign (Sep 08, 2023)
19-19096194-G-A			Uncertain significance (Dec 03, 2021)
19-19096196-C-T			Likely benign (Apr 06, 2023)
19-19096204-A-C			Uncertain significance (Mar 23, 2022)
19-19096208-AAG-A			Uncertain significance (Oct 17, 2022)
19-19096211-T-G			Uncertain significance (Oct 17, 2022)
19-19096212-A-ACCCCGGCCTCCTGGGATGGGTGTTCTCCTGGGG			Benign (Jan 26, 2024)
19-19096217-G-A			Likely benign (Nov 25, 2023)
19-19096308-T-A			Benign (May 25, 2021)
19-19101764-C-G			Likely benign (Jun 20, 2022)
19-19101767-A-G			Likely benign (Jul 03, 2023)
19-19101769-G-A			Likely benign (Jun 21, 2023)
19-19101777-G-A			Likely benign (May 15, 2022)
19-19101782-G-A		Inborn genetic diseases	Uncertain significance (May 03, 2023)
19-19101808-C-T			Likely benign (Dec 13, 2023)
19-19101810-G-T			Likely benign (Nov 24, 2023)

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