POLGARF

POLG alternative reading frame

Basic information

Region (hg38): 15:89330207-89333809

Links

ENSG00000291307 ∙ NCBI:125316803 ∙ ∙ HGNC:56246 ∙ Uniprot:A0A3B3IS91 ∙ 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 POLGARF gene.

• Progressive sclerosing poliodystrophy (395 variants)
• not provided (156 variants)
• Inborn genetic diseases (52 variants)
• not specified (51 variants)
• 6 conditions (17 variants)
• Hereditary spastic paraplegia (16 variants)
• POLG-Related Spectrum Disorders (13 variants)
• POLG-related condition (8 variants)
• Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1 (3 variants)
• Mitochondrial disease (3 variants)
• Intellectual disability (3 variants)
• Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis (3 variants)
• Mitochondrial DNA depletion syndrome 4b (3 variants)
• Primary progressive multiple sclerosis;Mitochondrial DNA depletion syndrome (2 variants)
• Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 (1 variants)
• Progressive sclerosing poliodystrophy;Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1;Mitochondrial DNA depletion syndrome 4b (1 variants)
• Abnormality of corpus callosum (1 variants)
• See cases (1 variants)
• Progressive sclerosing poliodystrophy;Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1;Mitochondrial DNA depletion syndrome 4b;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 (1 variants)
• Seizure;Autism (1 variants)
• Mitochondrial DNA depletion syndrome 1 (1 variants)
• Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1;Progressive sclerosing poliodystrophy;Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis;Mitochondrial DNA depletion syndrome 4b (1 variants)
• Mitochondrial neurogastrointestinal encephalomyopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLGARF 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	1	3	84	10	1	99
missense	8	10	118	93	2	231
nonsense				3		3
start loss						0
frameshift	4	5	1			10
inframe indel			39	18	1	58
splice donor/acceptor (+/-2bp)	1	1				2
splice region			2	3		5
non coding				12	5	17
Total	14	19	242	136	9

Highest pathogenic variant AF is 0.0000131

Variants in POLGARF

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

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

Position	Type	Phenotype	Significance	ClinVar
15-89330210-A-T		Progressive sclerosing poliodystrophy	Conflicting classifications of pathogenicity (Jan 21, 2024)
15-89330211-G-T		Progressive sclerosing poliodystrophy	Uncertain significance (Aug 31, 2023)
15-89330213-C-T		not specified • Progressive sclerosing poliodystrophy	Likely benign (Jun 27, 2023)
15-89330214-G-A		Progressive sclerosing poliodystrophy	Likely benign (May 18, 2023)
15-89330216-C-T		Progressive sclerosing poliodystrophy	Likely benign (May 12, 2023)
15-89330217-G-A		Progressive sclerosing poliodystrophy • 6 conditions	Uncertain significance (Jan 15, 2024)
15-89330218-A-G		Progressive sclerosing poliodystrophy	Uncertain significance (Mar 10, 2021)
15-89330219-C-T		Progressive sclerosing poliodystrophy • POLG-related disorder	Likely benign (Jan 10, 2024)
15-89330223-T-C		Progressive sclerosing poliodystrophy	Uncertain significance (Jun 29, 2023)
15-89330231-C-T		Progressive sclerosing poliodystrophy	Pathogenic (Oct 01, 2018)
15-89330234-A-G		Progressive sclerosing poliodystrophy	Likely benign (Apr 21, 2021)
15-89330237-G-GT		Progressive sclerosing poliodystrophy	Pathogenic (Oct 01, 2018)
15-89330241-C-G		Progressive sclerosing poliodystrophy	Uncertain significance (Aug 10, 2022)
15-89330241-C-T		Mitochondrial disease • Progressive sclerosing poliodystrophy	Pathogenic (Jan 07, 2024)
15-89330242-G-A			Pathogenic (May 18, 2015)
15-89330245-C-T		Progressive sclerosing poliodystrophy	Uncertain significance (Oct 25, 2022)
15-89330249-C-T		Progressive sclerosing poliodystrophy	Likely benign (May 25, 2022)
15-89330252-C-T		Progressive sclerosing poliodystrophy	Likely benign (Jul 14, 2023)
15-89330256-C-T		Progressive sclerosing poliodystrophy	Uncertain significance (Oct 07, 2023)
15-89330257-G-A		Abnormality of corpus callosum • Progressive sclerosing poliodystrophy • Inborn genetic diseases • Mitochondrial DNA depletion syndrome 4b	Pathogenic/Likely pathogenic (Jan 20, 2024)
15-89330258-C-G		Progressive sclerosing poliodystrophy • Autism;Seizure • Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis • Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1 • Inborn genetic diseases • POLG-Related Spectrum Disorders • not specified	Conflicting classifications of pathogenicity (Jan 30, 2024)
15-89330263-T-C		Progressive sclerosing poliodystrophy	Uncertain significance (Jul 31, 2023)
15-89330270-G-A		Progressive sclerosing poliodystrophy	Likely benign (Dec 02, 2021)
15-89330273-A-G		Progressive sclerosing poliodystrophy	Likely benign (May 21, 2018)
15-89330276-C-T		Progressive sclerosing poliodystrophy	Pathogenic (May 02, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP