SLC25A23

solute carrier family 25 member 23, the group of Solute carrier family 25|EF-hand domain containing

Basic information

Region (hg38): 19:6436078-6465203

Links

ENSG00000125648 ∙ NCBI:79085 ∙ OMIM:608746 ∙ HGNC:19375 ∙ Uniprot:Q9BV35 ∙ 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 SLC25A23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A23 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	3	4
missense			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	2	3

Variants in SLC25A23

This is a list of pathogenic ClinVar variants found in the SLC25A23 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-6442006-A-G		not specified	Uncertain significance (Feb 17, 2024)
19-6442024-T-C		not specified	Uncertain significance (Aug 02, 2023)
19-6442049-C-A		not specified	Uncertain significance (Mar 05, 2024)
19-6442076-G-A		not specified	Uncertain significance (Aug 08, 2023)
19-6442088-G-A		not specified	Likely benign (Sep 16, 2021)
19-6442124-C-A		not specified	Uncertain significance (Dec 19, 2022)
19-6444184-G-C		not specified	Uncertain significance (Apr 09, 2024)
19-6444210-G-T		not specified	Uncertain significance (Mar 24, 2023)
19-6444247-T-C		not specified	Uncertain significance (May 23, 2023)
19-6452315-G-A			Benign (Oct 19, 2017)
19-6452353-C-A		not specified	Uncertain significance (Aug 24, 2023)
19-6452374-C-T		not specified	Uncertain significance (Jan 31, 2024)
19-6452413-G-A		not specified	Uncertain significance (Jun 05, 2023)
19-6452448-G-A		not specified	Uncertain significance (Apr 01, 2024)
19-6452454-C-T		not specified	Uncertain significance (Sep 27, 2022)
19-6452455-G-A		not specified	Uncertain significance (Aug 02, 2021)
19-6454034-C-T		not specified	Uncertain significance (Oct 13, 2023)
19-6454057-G-A		not specified	Uncertain significance (Sep 20, 2023)
19-6454335-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-6454355-C-T		not specified	Uncertain significance (Oct 13, 2023)
19-6454361-C-T			not provided (-)
19-6454388-C-T		not specified	Uncertain significance (Jan 04, 2022)
19-6454390-C-T		not specified	Uncertain significance (May 09, 2023)
19-6454440-A-G			Likely benign (Feb 01, 2023)
19-6454453-C-T		not specified	Uncertain significance (Jul 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A23	protein_coding	protein_coding	ENST00000301454	10	29125

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00206	0.997	125576	1	171	125748	0.000684

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	221	305	0.726	0.0000195	2995
Missense in Polyphen		95	136.78	0.69457		1292
Synonymous	0.193	120	123	0.978	0.00000772	961
Loss of Function	2.93	9	24.7	0.364	0.00000130	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00745	0.00695
European (Non-Finnish)	0.000143	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent mitochondrial solute carrier. Mitochondrial solute carriers shuttle metabolites, nucleotides, and cofactors through the mitochondrial inner membrane (PubMed:15123600). May act as a ATP-Mg/Pi exchanger that mediates the transport of Mg-ATP in exchange for phosphate, catalyzing the net uptake or efflux of adenine nucleotides into or from the mitochondria (PubMed:15123600). Acts as a regulator of mitochondrial calcium uptake via interaction with MCU and MICU1 (PubMed:24430870). {ECO:0000269|PubMed:15123600, ECO:0000269|PubMed:24430870}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.257
• rvis_EVS: -1.02
• rvis_percentile_EVS: 8

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.493
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.197

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a23
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: regulation of oxidative phosphorylation;mitochondrial calcium ion transmembrane transport;ATP transport;calcium import into the mitochondrion;regulation of cellular respiration;regulation of sequestering of calcium ion;cellular response to calcium ion;urea homeostasis
• Cellular component: mitochondrion;mitochondrial inner membrane;integral component of membrane
• Molecular function: ATP transmembrane transporter activity;calcium ion binding;protein binding