SLC25A25

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

Basic information

Region (hg38): 9:128068200-128109245

Links

ENSG00000148339 ∙ NCBI:114789 ∙ OMIM:608745 ∙ HGNC:20663 ∙ Uniprot:Q6KCM7 ∙ 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 SLC25A25 gene.

• Inborn genetic diseases (11 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A25 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	1	2
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	1

Variants in SLC25A25

This is a list of pathogenic ClinVar variants found in the SLC25A25 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128068507-G-A		not specified	Uncertain significance (Oct 26, 2021)
9-128101187-G-A		not specified	Uncertain significance (Aug 02, 2023)
9-128101332-A-T		not specified	Uncertain significance (Jan 04, 2022)
9-128102084-C-T		High myopia	Uncertain significance (Dec 17, 2018)
9-128102372-T-C		not specified	Uncertain significance (Aug 07, 2023)
9-128103700-A-G		not specified	Uncertain significance (May 08, 2023)
9-128105741-C-T		not specified	Uncertain significance (Dec 14, 2023)
9-128105813-C-T		not specified	Uncertain significance (Mar 08, 2024)
9-128105829-A-G		not specified	Uncertain significance (Aug 16, 2021)
9-128106157-G-A		not specified	Uncertain significance (Oct 29, 2021)
9-128106195-G-A		not specified	Uncertain significance (Aug 09, 2021)
9-128106391-G-C		Nephrolithiasis	Pathogenic (Jan 01, 2020)
9-128106437-G-C		not specified	Uncertain significance (Jan 20, 2023)
9-128106441-T-G		not specified	Uncertain significance (Mar 24, 2023)
9-128107173-G-A		not specified	Uncertain significance (Dec 02, 2022)
9-128107273-C-T			Likely benign (Apr 16, 2018)
9-128107279-G-A			Benign (Apr 16, 2018)
9-128107437-C-T		not specified	Uncertain significance (Nov 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A25	protein_coding	protein_coding	ENST00000373068	10	41045

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0240	0.975	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	224	305	0.734	0.0000183	3257
Missense in Polyphen		60	94.94	0.63198		1032
Synonymous	0.514	126	134	0.943	0.00000886	1025
Loss of Function	3.03	7	22.5	0.311	0.00000103	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000887	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent mitochondrial solute carrier. Mitochondrial solute carriers shuttle metabolites, nucleotides, and cofactors through the mitochondrial inner membrane. 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. {ECO:0000269|PubMed:15123600}.

Recessive Scores

• pRec: 0.0959

Intolerance Scores

• loftool: 0.161
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.119
• hipred: Y
• hipred_score: 0.728
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a25
• Phenotype: vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: response to dietary excess;response to activity;ATP transport;response to food;multicellular organism growth;camera-type eye development;cellular respiration;ATP metabolic process;adipose tissue development;calcium ion transmembrane transport
• Cellular component: mitochondrial inner membrane;integral component of membrane
• Molecular function: ATP transmembrane transporter activity;calcium ion binding