SLC25A52

solute carrier family 25 member 52, the group of Solute carrier family 25

Basic information

Region (hg38): 18:31759584-31760880

Previous symbols: [ "MCART2" ]

Links

ENSG00000141437 ∙ NCBI:147407 ∙ OMIM:616153 ∙ HGNC:23324 ∙ Uniprot:Q3SY17 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A52 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A52 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						0
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in SLC25A52

This is a list of pathogenic ClinVar variants found in the SLC25A52 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-31760235-T-C		not specified	Uncertain significance (Nov 11, 2024)
18-31760339-A-G		not specified	Uncertain significance (Aug 16, 2022)
18-31760355-C-T		not specified	Uncertain significance (Apr 26, 2024)
18-31760427-T-A		not specified	Uncertain significance (Feb 09, 2023)
18-31760450-T-C		not specified	Uncertain significance (Apr 19, 2024)
18-31760576-C-G		not specified	Uncertain significance (Aug 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A52	protein_coding	protein_coding	ENST00000269205	1	1319

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000502	0.462	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0905	171	174	0.981	0.0000101	2002
Missense in Polyphen		51	50.723	1.0055		615
Synonymous	0.369	61	64.8	0.942	0.00000346	630
Loss of Function	0.141	5	5.35	0.934	3.73e-7	75

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0956

Intolerance Scores

• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.46

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Gene ontology

• Biological process: transmembrane transport
• Cellular component: mitochondrial inner membrane;integral component of membrane
• Molecular function: transmembrane transporter activity