SLC25A16

solute carrier family 25 member 16, the group of Solute carrier family 25

Basic information

Region (hg38): 10:68477997-68527523

Links

ENSG00000122912 ∙ NCBI:8034 ∙ OMIM:139080 ∙ HGNC:10986 ∙ Uniprot:P16260 ∙ 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 SLC25A16 gene.

• Inborn genetic diseases (15 variants)
• Cerebral visual impairment and intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A16 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		1	15			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	15	0	0

Highest pathogenic variant AF is 0.0000132

Variants in SLC25A16

This is a list of pathogenic ClinVar variants found in the SLC25A16 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-68483497-T-G		not specified	Uncertain significance (May 16, 2023)
10-68483526-C-T		not specified	Uncertain significance (Aug 04, 2023)
10-68483543-A-C		not specified	Uncertain significance (Aug 23, 2021)
10-68483559-T-C		not specified	Uncertain significance (Aug 28, 2023)
10-68483580-C-T		not specified	Uncertain significance (Oct 05, 2021)
10-68487189-C-T		not specified	Uncertain significance (Apr 14, 2022)
10-68487192-C-T		not specified	Uncertain significance (Feb 22, 2023)
10-68487193-G-A		Cerebral visual impairment and intellectual disability	Likely pathogenic (Sep 09, 2015)
10-68488468-A-G		not specified	Uncertain significance (Dec 13, 2022)
10-68488483-T-C		not specified	Uncertain significance (Feb 28, 2024)
10-68488557-G-A		not specified	Uncertain significance (Aug 21, 2023)
10-68493523-G-A		not specified	Uncertain significance (Aug 12, 2021)
10-68506590-T-C		not specified	Uncertain significance (Oct 03, 2022)
10-68506655-T-C		not specified	Uncertain significance (Sep 13, 2023)
10-68516765-T-A		not specified	Uncertain significance (Mar 01, 2023)
10-68516796-C-G		not specified	Uncertain significance (Sep 29, 2022)
10-68527272-T-C		not specified	Uncertain significance (Jul 20, 2022)
10-68527284-C-A		Inherited isolated nail anomaly • autosomal recessive isolated fingernail dysplasia	Conflicting classifications of pathogenicity (Jun 12, 2018)
10-68527333-G-A		not specified	Uncertain significance (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A16	protein_coding	protein_coding	ENST00000609923	9	49476

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000121	0.824	125712	0	28	125740	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.580	160	182	0.879	0.00000959	2109
Missense in Polyphen		53	73.241	0.72364		836
Synonymous	-0.147	63	61.5	1.02	0.00000302	673
Loss of Function	1.41	12	18.5	0.647	0.00000114	220

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000294	0.000294
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000559	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.0000559	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the accumulation of coenzyme A in the mitochondrial matrix. {ECO:0000269|PubMed:11158296}.
• Pathway: Coenzyme A biosynthesis;Vitamin B5 - CoA biosynthesis from pantothenate;Metabolism;Vitamin B5 (pantothenate) metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.584
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.0788
• hipred: N
• hipred_score: 0.346
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.183

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a16

Gene ontology

• Biological process: mitochondrial transport;coenzyme biosynthetic process;transmembrane transport
• Cellular component: mitochondrion;mitochondrial inner membrane;integral component of membrane
• Molecular function: secondary active transmembrane transporter activity;antiporter activity