SLC25A29

solute carrier family 25 member 29, the group of Solute carrier family 25

Basic information

Region (hg38): 14:100291116-100306547

Previous symbols: [ "C14orf69" ]

Links

ENSG00000197119 ∙ NCBI:123096 ∙ OMIM:615064 ∙ HGNC:20116 ∙ Uniprot:Q8N8R3 ∙ 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 SLC25A29 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A29 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				2		2
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	20	2	0

Variants in SLC25A29

This is a list of pathogenic ClinVar variants found in the SLC25A29 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-100292296-G-C		not specified	Uncertain significance (Feb 14, 2023)
14-100292302-G-A		not specified	Uncertain significance (Jul 20, 2021)
14-100292317-G-A		not specified	Uncertain significance (May 10, 2022)
14-100292342-C-T		not specified	Uncertain significance (Feb 24, 2022)
14-100292354-C-G		not specified	Uncertain significance (Aug 23, 2021)
14-100292355-C-G		not specified	Uncertain significance (Apr 05, 2023)
14-100292357-C-T		not specified	Uncertain significance (Jul 12, 2023)
14-100292390-C-T		not specified	Uncertain significance (Mar 27, 2023)
14-100292395-G-A		not specified	Uncertain significance (Aug 08, 2022)
14-100292404-G-A		not specified	Uncertain significance (Nov 17, 2023)
14-100292417-G-T		not specified	Uncertain significance (Oct 26, 2022)
14-100292470-T-G		not specified	Uncertain significance (May 09, 2022)
14-100292476-C-T		not specified	Uncertain significance (Aug 21, 2024)
14-100292533-C-T		not specified	Uncertain significance (Dec 06, 2022)
14-100292651-C-T		not specified	Uncertain significance (Jun 29, 2023)
14-100292676-G-A			Likely benign (Oct 01, 2022)
14-100292699-C-A		not specified	Uncertain significance (Dec 07, 2023)
14-100292751-A-C			Likely benign (Oct 01, 2022)
14-100292775-C-G		not specified	Uncertain significance (Dec 04, 2024)
14-100292890-G-C		not specified	Uncertain significance (Aug 02, 2021)
14-100292921-G-A		not specified	Uncertain significance (Mar 06, 2023)
14-100292975-C-T		not specified	Uncertain significance (Sep 24, 2024)
14-100293338-G-A		not specified	Uncertain significance (Apr 06, 2023)
14-100293368-G-T		not specified	Uncertain significance (Apr 24, 2023)
14-100298874-C-T		not specified	Uncertain significance (Sep 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A29	protein_coding	protein_coding	ENST00000359232	4	15437

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00109	0.843	125296	0	60	125356	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.765	179	210	0.852	0.0000162	1834
Missense in Polyphen		66	97.729	0.67534		865
Synonymous	1.31	88	105	0.837	0.00000904	680
Loss of Function	1.22	6	10.2	0.587	5.36e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000228	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000541	0.0000462
European (Non-Finnish)	0.000380	0.000318
Middle Eastern	0.0000545	0.0000544
South Asian	0.000567	0.000523
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transports arginine, lysine, homoarginine, methylarginine and, to a much lesser extent, ornithine and histidine (PubMed:24652292). Can restore ornithine transport in cells lacking the primary mitochondrial ornithine transporter SLC25A15 (PubMed:19287344). Does not transport carnitine nor acylcarnitines (PubMed:24652292). Functions by both counter- exchange and uniport mechanisms (PubMed:24652292). {ECO:0000269|PubMed:19287344, ECO:0000269|PubMed:24652292}.
• Pathway: Thermogenesis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.154

Haploinsufficiency Scores

• pHI: 0.342
• hipred: N
• hipred_score: 0.398
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.153

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a29

Gene ontology

• Biological process: acyl carnitine transport;amino acid transport;ornithine transport;carnitine transport;L-histidine transmembrane transport;acyl carnitine transmembrane transport;L-arginine transmembrane transport;L-lysine transmembrane transport;mitochondrial L-ornithine transmembrane transport
• Cellular component: mitochondrion;mitochondrial inner membrane;integral component of membrane
• Molecular function: high-affinity arginine transmembrane transporter activity;high-affinity lysine transmembrane transporter activity;basic amino acid transmembrane transporter activity;acyl carnitine transmembrane transporter activity