SLC25A21

solute carrier family 25 member 21, the group of Solute carrier family 25|MicroRNA protein coding host genes

Basic information

Region (hg38): 14:36677920-37172606

Links

ENSG00000183032 ∙ NCBI:89874 ∙ OMIM:607571 ∙ HGNC:14411 ∙ Uniprot:Q9BQT8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial DNA depletion syndrome 18 (Limited), mode of inheritance: AR
• mitochondrial DNA depletion syndrome 18 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial DNA depletion syndrome 18	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; Neurologic	29517768

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A21 gene.

• Mitochondrial DNA depletion syndrome 18 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A21 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				13		13
missense			39	5	5	49
nonsense	1		2	1		4
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)			2			2
splice region			4	2	2	8
non coding				16	10	26
Total	1	0	45	35	15

Highest pathogenic variant AF is 0.0000395

Variants in SLC25A21

This is a list of pathogenic ClinVar variants found in the SLC25A21 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-36680661-C-A			Benign (Jan 24, 2024)
14-36680698-A-T		not specified	Uncertain significance (Jul 19, 2022)
14-36680699-C-T			Uncertain significance (Oct 27, 2023)
14-36680704-A-G		not specified	Uncertain significance (Apr 19, 2024)
14-36680724-A-G			Likely benign (Nov 24, 2023)
14-36680738-G-GT			Benign (Jan 31, 2024)
14-36683843-T-C			Uncertain significance (Nov 10, 2021)
14-36683852-G-A		not specified	Uncertain significance (Jun 23, 2021)
14-36684722-AAATAAG-A			Likely benign (Sep 22, 2022)
14-36684735-T-C			Likely benign (Oct 15, 2021)
14-36684751-C-G			Uncertain significance (Jul 11, 2022)
14-36684767-C-A		not specified	Uncertain significance (Aug 28, 2023)
14-36684769-T-A			Uncertain significance (Jun 28, 2022)
14-36684769-T-C		not specified	Uncertain significance (May 31, 2022)
14-36684771-G-A			Uncertain significance (Aug 10, 2022)
14-36684796-T-A		not specified	Uncertain significance (Jun 24, 2022)
14-36684802-C-G		not specified	Uncertain significance (Mar 18, 2024)
14-36684823-G-A			Uncertain significance (Nov 21, 2022)
14-36684834-T-C		Mitochondrial DNA depletion syndrome 18	Pathogenic (Jun 28, 2023)
14-36684861-A-T			Uncertain significance (Nov 15, 2022)
14-36684865-A-G			Uncertain significance (Dec 22, 2022)
14-36684871-T-C			Uncertain significance (Mar 18, 2022)
14-36684877-C-T			Uncertain significance (Nov 13, 2023)
14-36684878-C-T			Likely benign (Dec 22, 2023)
14-36684893-C-A			Likely benign (Feb 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A21	protein_coding	protein_coding	ENST00000331299	10	494436

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.45e-11	0.0548	125602	0	145	125747	0.000577

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0246	149	150	0.994	0.00000681	1905
Missense in Polyphen		73	67.007	1.0894		903
Synonymous	-0.375	57	53.5	1.07	0.00000254	569
Loss of Function	0.120	17	17.5	0.969	9.04e-7	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000479	0.000478
Ashkenazi Jewish	0.00180	0.00179
East Asian	0.00247	0.00239
Finnish	0.000279	0.000277
European (Non-Finnish)	0.000331	0.000325
Middle Eastern	0.00247	0.00239
South Asian	0.000842	0.000817
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transports C5-C7 oxodicarboxylates across the inner membranes of mitochondria. Can transport 2-oxoadipate, 2- oxoglutarate, adipate, glutarate, and to a lesser extent, pimelate, 2-oxopimelate, 2-aminoadipate, oxaloacetate, and citrate.
• Pathway: Lysine catabolism;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;Metabolism of amino acids and derivatives;Metabolism;Lysine metabolism (Consensus)

Recessive Scores

• pRec: 0.267

Intolerance Scores

• loftool: 0.617
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.08

Haploinsufficiency Scores

• pHI: 0.315
• hipred: N
• hipred_score: 0.351

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.336

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a21
• 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); craniofacial phenotype; homeostasis/metabolism phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: lysine catabolic process;alpha-ketoglutarate transport;transmembrane transport
• Cellular component: mitochondrial inner membrane;integral component of membrane
• Molecular function: alpha-ketoglutarate transmembrane transporter activity