SLC25A24

solute carrier family 25 member 24, the group of Solute carrier family 25|EF-hand domain containing

Basic information

Region (hg38): 1:108134042-108200849

Links

ENSG00000085491 ∙ NCBI:29957 ∙ OMIM:608744 ∙ HGNC:20662 ∙ Uniprot:Q6NUK1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Fontaine progeroid syndrome (Strong), mode of inheritance: AD
• Fontaine progeroid syndrome (Supportive), mode of inheritance: AR
• Fontaine progeroid syndrome (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Fontaine progeroid syndrome	AD	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	Craniofacial; Dermatologic; Genitourinary; Musculoskeletal	21216154; 29100093; 29100094

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A24 gene.

• Fontaine progeroid syndrome (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A24 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				11	5	16
missense	2	1	46	5	4	58
nonsense			2	2		4
start loss			1			1
frameshift			2	3		5
inframe indel				1		1
splice donor/acceptor (+/-2bp)			3			3
splice region				4		4
non coding				5	26	31
Total	2	1	54	27	35

Variants in SLC25A24

This is a list of pathogenic ClinVar variants found in the SLC25A24 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-108136529-A-G			Benign (May 16, 2021)
1-108136654-C-A			Uncertain significance (Mar 01, 2024)
1-108136697-C-A		Inborn genetic diseases	Uncertain significance (Apr 20, 2023)
1-108136698-C-A			Likely benign (Dec 12, 2023)
1-108136702-T-C			Uncertain significance (Aug 11, 2020)
1-108136727-C-T		SLC25A24-related disorder	Uncertain significance (Aug 08, 2023)
1-108136741-G-A		Fontaine progeroid syndrome	Uncertain significance (-)
1-108136744-G-A		Inborn genetic diseases	Uncertain significance (Mar 18, 2024)
1-108136750-C-T		Inborn genetic diseases	Uncertain significance (May 01, 2022)
1-108136771-C-A		Inborn genetic diseases	Uncertain significance (Jan 04, 2024)
1-108136789-C-T		Inborn genetic diseases	Uncertain significance (Feb 13, 2023)
1-108136793-G-A			Likely benign (Nov 08, 2022)
1-108136801-C-T			Uncertain significance (Jul 05, 2022)
1-108136814-G-T		Dementia;Bilateral tonic-clonic seizure	Uncertain significance (Sep 06, 2019)
1-108136833-C-A		Inborn genetic diseases	Uncertain significance (Feb 05, 2024)
1-108136838-C-T			Uncertain significance (Dec 06, 2022)
1-108136840-A-G			Likely benign (Dec 01, 2020)
1-108136846-T-TA			Benign (Nov 12, 2023)
1-108136910-C-T			Benign (May 16, 2021)
1-108138860-G-T			Benign (May 16, 2021)
1-108138978-T-C			Benign (May 16, 2021)
1-108139059-TTGAGCCTGCA-T			Likely benign (Jan 15, 2024)
1-108139072-C-T			Uncertain significance (Nov 01, 2023)
1-108139078-C-T			Uncertain significance (Dec 17, 2022)
1-108139096-T-A			Uncertain significance (Jun 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A24	protein_coding	protein_coding	ENST00000565488	10	66814

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.35e-12	0.285	125537	0	211	125748	0.000839

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.824	220	257	0.855	0.0000125	3109
Missense in Polyphen		65	94.035	0.69123		1186
Synonymous	-0.663	99	91.0	1.09	0.00000462	901
Loss of Function	1.05	21	26.9	0.782	0.00000144	302

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00150	0.00150
Ashkenazi Jewish	0.00276	0.00268
East Asian	0.00171	0.00169
Finnish	0.00106	0.00106
European (Non-Finnish)	0.000551	0.000545
Middle Eastern	0.00171	0.00169
South Asian	0.000919	0.000915
Other	0.00183	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent mitochondrial solute carrier. Mediates the reversible, electroneutral exchange of Mg-ATP or Mg-ADP against phosphate ions, catalyzing the net uptake or efflux of adenine nucleotides across the mitochondrial inner membrane. Nucleotide transport is inactive when cytosolic calcium levels are low, and is activated by an increase in cytosolic calcium levels. May play a role in protecting cells against oxidative stress- induced cell death, probably by promoting the formation of calcium-phosphate precipitates in the mitochondrial matrix, and thereby buffering calcium levels in the mitochondrial matrix. {ECO:0000269|PubMed:15123600, ECO:0000269|PubMed:22015608, ECO:0000269|PubMed:29100093}.
• Disease: DISEASE: Fontaine progeroid syndrome (FPS) [MIM:612289]: An autosomal dominant progeroid disorder characterized by prenatal and postnatal growth retardation, decreased subcutaneous fat tissue, wrinkled skin, an aged appearance since birth, an abnormal scalp hair pattern, sparse hair, hypoplastic distal phalanges with hypoplastic nails, a widely open anterior fontanel, facial dysmorphisms, and craniosynostosis. Early death is observed in some patients. {ECO:0000269|PubMed:29100093}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.876
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.57

Haploinsufficiency Scores

• pHI: 0.167
• hipred: N
• hipred_score: 0.350
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.248

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a24

Gene ontology

• Biological process: mitochondrial transport;regulation of cell death;ATP transport;cellular response to oxidative stress;transmembrane transport;cellular response to calcium ion
• Cellular component: mitochondrion;mitochondrial inner membrane;integral component of membrane
• Molecular function: ATP transmembrane transporter activity;calcium ion binding