SLC25A48

solute carrier family 25 member 48, the group of Solute carrier family 25

Basic information

Region (hg38): 5:135476912-135889770

Links

ENSG00000145832 ∙ NCBI:153328 ∙ OMIM:616150 ∙ HGNC:30451 ∙ Uniprot:Q6ZT89 ∙ 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 SLC25A48 gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A48 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			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in SLC25A48

This is a list of pathogenic ClinVar variants found in the SLC25A48 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-135534996-C-T		not specified	Uncertain significance (Jan 26, 2023)
5-135535143-G-A		not specified	Uncertain significance (Mar 31, 2023)
5-135535143-G-C		not specified	Uncertain significance (Jun 09, 2022)
5-135535143-G-T			Benign (Mar 29, 2018)
5-135535168-C-G		not specified	Uncertain significance (May 03, 2023)
5-135535207-C-T		not specified	Uncertain significance (Oct 20, 2023)
5-135535210-G-A		not specified	Uncertain significance (Oct 22, 2021)
5-135535344-C-A		Cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delay	Pathogenic (Aug 16, 2023)
5-135535459-T-TCCGG		See cases • Cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delay	Likely pathogenic (Feb 17, 2021)
5-135535483-C-T		not specified	Uncertain significance (Dec 16, 2021)
5-135535489-C-A		Cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delay	Pathogenic (Aug 16, 2023)
5-135535503-C-A		not specified	Uncertain significance (Mar 02, 2023)
5-135535503-C-T		not specified	Uncertain significance (May 23, 2023)
5-135535550-C-T			Benign (Mar 29, 2018)
5-135535560-G-A		not specified	Uncertain significance (May 17, 2023)
5-135535576-C-T		not specified	Uncertain significance (Nov 12, 2021)
5-135535590-C-T			Benign (Dec 31, 2019)
5-135535642-T-C		not specified	Uncertain significance (Dec 09, 2023)
5-135535647-G-A		not specified	Uncertain significance (Mar 04, 2024)
5-135535648-C-A		not specified	Uncertain significance (Dec 14, 2023)
5-135574594-T-C		not specified	Uncertain significance (Feb 13, 2024)
5-135578438-C-T		not specified	Uncertain significance (Aug 26, 2022)
5-135578470-T-C		not specified	Uncertain significance (Jul 26, 2022)
5-135578760-C-T		not specified	Uncertain significance (Apr 05, 2023)
5-135578763-C-T		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A48	protein_coding	protein_coding	ENST00000412661	5	53989

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000152	0.445	124752	0	26	124778	0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.787	86	109	0.788	0.00000722	1023
Missense in Polyphen		28	38.484	0.72758		397
Synonymous	0.605	39	44.1	0.884	0.00000306	318
Loss of Function	0.236	6	6.66	0.901	2.83e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000140	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000505	0.000445
Finnish	0.000171	0.000139
European (Non-Finnish)	0.000118	0.000106
Middle Eastern	0.000505	0.000445
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.440
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a48

Gene ontology

• Biological process: acyl carnitine transport;acyl carnitine transmembrane transport
• Cellular component: mitochondrial inner membrane;integral component of membrane
• Molecular function: protein binding;acyl carnitine transmembrane transporter activity