chr15-62013057-T-TTCTG

Variant names:

• chr15-62013057-T-TTCTG
• rs879253853
• NM_020821.3:c.806_807insCAGA

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_020821.3(VPS13C):​c.806_807insCAGA​(p.Arg269SerfsTer14) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: VPS13C NM_020821.3 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 1.04
• Publications: 2 publications found

Genes affected

VPS13C (HGNC:23594): (vacuolar protein sorting 13 homolog C) Involved in mitochondrion organization and negative regulation of parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization. Located in cytosol and mitochondrial outer membrane. Implicated in Parkinson's disease 23. [provided by Alliance of Genome Resources, Apr 2022]

VPS13C Gene-Disease associations (from GenCC):

• autosomal recessive early-onset Parkinson disease 23

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• young-onset Parkinson disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Pathogenic. The variant received 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 15-62013057-T-TTCTG is Pathogenic according to our data. Variant chr15-62013057-T-TTCTG is described in ClinVar as Pathogenic. ClinVar VariationId is 222068.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VPS13C	NM_020821.3	c.806_807insCAGA	p.Arg269SerfsTer14	frameshift_variant	Exon 11 of 85	ENST00000644861.2	NP_065872.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VPS13C	ENST00000644861.2	c.806_807insCAGA	p.Arg269SerfsTer14	frameshift_variant	Exon 11 of 85		NM_020821.3	ENSP00000493560.2
VPS13C	ENST00000249837.7	c.677_678insCAGA	p.Arg226SerfsTer14	frameshift_variant	Exon 9 of 83	1		ENSP00000249837.3
VPS13C	ENST00000395898.3	c.677_678insCAGA	p.Arg226SerfsTer14	frameshift_variant	Exon 9 of 80	1		ENSP00000379235.3
VPS13C	ENST00000645819.1	c.806_807insCAGA	p.Arg269SerfsTer14	frameshift_variant	Exon 11 of 82			ENSP00000496179.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Parkinson disease Pathogenic:1

Nov 16, 2015

Brain and Spine Institute, INSERM

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.0
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs879253853; hg19: chr15-62305256;