SLC25A16

protein-coding

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

Gene summary

This gene encodes a protein that contains three tandemly repeated mitochondrial carrier protein domains. The encoded protein is localized in the inner membrane and facilitates the rapid transport and exchange of molecules between the cytosol and the mitochondrial matrix space. This gene has a possible role in Graves' disease. [provided by RefSeq, Jul 2008]

MANE transcript

NM_152707.4

Inheritance

—

ClinVar variants

P:2U:47B:1

Top phenotype

Cerebral visual impairment and intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr10:68,477,998-68,527,523

External References & Databases

Ensembl (ENSG00000122912)

Transcript & Mutation Effects

hg38 • Region Span ~49.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC25A16 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 1

Cerebral visual impairment and intellectual disabilityTotal: 1

Inherited isolated nail anomalyTotal: 1

autosomal recessive isolated fingernail dysplasiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152707.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense		2 clinvar	45 clinvar	1 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	2	47	1	0	50

Highest pathogenic variant AF is 0.000010029372

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152707.4	RefSeq	NP_689920.1	9	MANE Select
ENST00000609923.6	Ensembl	ENSP00000476815.1	9	MANE Select
NM_001324312.2	RefSeq	NP_001311241.1	9	Standard
NM_001324313.2	RefSeq	NP_001311242.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Coenzyme A biosynthesis
Vitamin B5 - CoA biosynthesis from pantothenate
Metabolism
Vitamin B5 (pantothenate) metabolism
Metabolism of water-soluble vitamins and cofactors

Biological Process

mitochondrial transport
coenzyme biosynthetic process
transmembrane transport

Molecular Function

secondary active transmembrane transporter activity
antiporter activity

Cellular Component

mitochondrion
mitochondrial inner membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000609923
Coding exons: 9
Length: 49476
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 28
Defined: 125740
p: 0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.580	160	182	0.879	0.00000959	2109
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00023	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for the accumulation of coenzyme A in the mitochondrial matrix. {ECO:0000269|PubMed:11158296}.;

Recessive Scores

pRec: 0.127

Intolerance Scores

LoFtool: 0.584
RVIS EVS: -0.43
RVIS percentile EVS: 25.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.183

Gene Damage Prediction

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