SLC25A33

solute carrier family 25 member 33, the group of Solute carrier family 25

Basic information

Region (hg38): 1:9539465-9585173

Links

ENSG00000171612 ∙ NCBI:84275 ∙ OMIM:610816 ∙ HGNC:29681 ∙ Uniprot:Q9BSK2 ∙ 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 SLC25A33 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A33 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in SLC25A33

This is a list of pathogenic ClinVar variants found in the SLC25A33 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-9539725-C-G		not specified	Uncertain significance (Jan 27, 2025)
1-9539736-C-T		SLC25A33-related disorder	Likely benign (Jun 25, 2024)
1-9553682-G-A		not specified	Uncertain significance (Apr 27, 2024)
1-9553707-C-T		SLC25A33-related disorder	Benign (Dec 20, 2019)
1-9553718-A-G		not specified	Uncertain significance (Oct 12, 2024)
1-9553724-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-9567285-T-A		not specified	Uncertain significance (Jun 28, 2022)
1-9567286-C-G		not specified	Uncertain significance (Jun 28, 2022)
1-9567330-G-A		not specified	Uncertain significance (Nov 25, 2024)
1-9567341-G-T		not specified	Uncertain significance (Aug 27, 2024)
1-9567343-T-C		not specified	Uncertain significance (Dec 12, 2024)
1-9570268-T-G		not specified	Uncertain significance (Mar 25, 2024)
1-9570283-A-G		not specified	Uncertain significance (Apr 18, 2023)
1-9570313-G-A		not specified	Uncertain significance (Jan 30, 2024)
1-9570353-C-T		not specified	Uncertain significance (May 12, 2024)
1-9573348-T-C		not specified	Uncertain significance (Nov 19, 2022)
1-9573384-G-C		not specified	Uncertain significance (Nov 21, 2023)
1-9573407-A-G		SLC25A33-related disorder	Benign (May 14, 2019)
1-9579970-C-A		not specified	Uncertain significance (Oct 01, 2024)
1-9580012-G-A		not specified	Uncertain significance (Oct 11, 2024)
1-9580021-C-T		not specified	Uncertain significance (Jan 31, 2024)
1-9580093-G-A		not specified	Uncertain significance (Jan 21, 2025)
1-9582311-C-T		not specified	Uncertain significance (Nov 12, 2024)
1-9582328-G-A		not specified	Uncertain significance (Aug 26, 2022)
1-9582336-G-A		SLC25A33-related disorder	Likely benign (Dec 20, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A33	protein_coding	protein_coding	ENST00000302692	7	45697

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00592	0.975	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.835	144	175	0.822	0.0000100	2038
Missense in Polyphen		75	99.38	0.75468		1036
Synonymous	-0.565	70	64.2	1.09	0.00000359	658
Loss of Function	2.04	6	14.4	0.418	6.85e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000930	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000659	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial transporter that imports/exports pyrimidine nucleotides into and from mitochondria (PubMed:25320081). Transports preferentially uracil, thymine, and cytosine (deoxy)nucleoside di- and triphosphates by an antiport mechanism (PubMed:25320081). Also transports guanine but not adenine (deoxy)nucleotides (PubMed:25320081). Is inhibited strongly by pyridoxal 5'-phosphate, 4,7-diphenyl-1,10- phenanthroline, tannic acid, and mercurials (mercury dichloride, mersalyl acid, p-hydroxymercuribenzoate) (PubMed:25320081). Participates in mitochondrial genome maintenance, regulation of mitochondrial membrane potential and mitochondrial respiration (PubMed:20453889). Upon INS or IGF1 stimulation regulates cell growth and proliferation by controlling mitochondrial DNA replication and transcription, the ratio of mitochondria-to nuclear-encoded components of the electron transport chain resulting in control of mitochondrial ROS production (PubMed:20453889, PubMed:17596519). Participates in dendritic cell endocytosis and may associate with mitochondrial oxidative phosphorylation (PubMed:14715278). {ECO:0000269|PubMed:14715278, ECO:0000269|PubMed:17596519, ECO:0000269|PubMed:20453889, ECO:0000269|PubMed:25320081}.

Recessive Scores

• pRec: 0.0876

Intolerance Scores

• loftool: 0.424
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.110
• hipred: Y
• hipred_score: 0.699
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a33

Gene ontology

• Biological process: mitochondrial genome maintenance;regulation of oxidative phosphorylation;mitochondrial transcription;pyrimidine nucleotide transport;mitochondrion organization;positive regulation of cell population proliferation;positive regulation of cell growth;mitochondria-nucleus signaling pathway;cellular response to insulin stimulus;mitochondrial respiratory chain complex III assembly;regulation of mitochondrial membrane potential;regulation of cell cycle arrest;regulation of reactive oxygen species biosynthetic process;cellular response to insulin-like growth factor stimulus;pyrimidine nucleotide import into mitochondrion
• Cellular component: mitochondrial inner membrane;integral component of membrane;mitochondrial membrane
• Molecular function: pyrimidine nucleotide transmembrane transporter activity