chr9-136412024-TA-T

Variant names:

• chr9-136412024-TA-T
• NM_015160.3:c.100delA

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_015160.3(PMPCA):​c.100delA​(p.Ser34ValfsTer36) variant causes a frameshift change. 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: 33)
• Consequence: PMPCA NM_015160.3 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 6.61

Genes affected

PMPCA (HGNC:18667): (peptidase, mitochondrial processing subunit alpha) The protein encoded by this gene is found in the mitochondrion, where it represents the alpha subunit of a proteolytic heterodimer. This heterodimer is responsible for cleaving the transit peptide from nuclear-encoded mitochondrial proteins. Defects in this gene are a cause of spinocerebellar ataxia, autosomal recessive 2. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Pathogenic. Variant got 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 9-136412024-TA-T is Pathogenic according to our data. Variant chr9-136412024-TA-T is described in ClinVar as [Pathogenic]. Clinvar id is 2722122.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PMPCA	NM_015160.3	c.100delA	p.Ser34ValfsTer36	frameshift_variant	Exon 2 of 13	ENST00000371717.8	NP_055975.1
PMPCA	XM_005266059.4	c.100delA	p.Ser34ValfsTer36	frameshift_variant	Exon 2 of 12		XP_005266116.1
PMPCA	NM_001282946.2	c.-199delA		5_prime_UTR_variant	Exon 2 of 13		NP_001269875.1
PMPCA	NM_001282944.2	c.-199delA		5_prime_UTR_variant	Exon 2 of 12		NP_001269873.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PMPCA	ENST00000371717.8	c.100delA	p.Ser34ValfsTer36	frameshift_variant	Exon 2 of 13	1	NM_015160.3	ENSP00000360782.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Nov 27, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Ser34Valfs*36) in the PMPCA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PMPCA are known to be pathogenic (PMID: 35885985). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PMPCA-related conditions. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-139306476;