2-27309851-TCTGACCGTTCCAGGGTCAAGCTGCATCACTGCAAGGTGGAAACGATGGAGTGAGGCAGGCTTAGAGCCGATGTGCCTTCCAGGACAGGTAGGAGTTCCAGATAACAGCAACACATTGGACAACGGCCAACCTAAGGAACAGGAATAAC-T

Variant summary

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

The NM_002437.5(MPV17):c.462-18_*60del variant causes a splice acceptor, coding sequence, 3 prime UTR, intron 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 (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: MPV17 NM_002437.5 splice_acceptor, coding_sequence, 3_prime_UTR, intron
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 0.750

Genes affected

MPV17 (HGNC:7224): (mitochondrial inner membrane protein MPV17) This gene encodes a mitochondrial inner membrane protein that is implicated in the metabolism of reactive oxygen species. Mutations in this gene have been associated with the hepatocerebral form of mitochondrial DNA depletion syndrome (MDDS). [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Splicing variant, LoF is a know mechanism of disease,
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 2-27309851-TCTGACCGTTCCAGGGTCAAGCTGCATCACTGCAAGGTGGAAACGATGGAGTGAGGCAGGCTTAGAGCCGATGTGCCTTCCAGGACAGGTAGGAGTTCCAGATAACAGCAACACATTGGACAACGGCCAACCTAAGGAACAGGAATAAC-T is Pathogenic according to our data. Variant chr2-27309851-TCTGACCGTTCCAGGGTCAAGCTGCATCACTGCAAGGTGGAAACGATGGAGTGAGGCAGGCTTAGAGCCGATGTGCCTTCCAGGACAGGTAGGAGTTCCAGATAACAGCAACACATTGGACAACGGCCAACCTAAGGAACAGGAATAAC-T is described in ClinVar as [Pathogenic]. Clinvar id is 2672805.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPV17	NM_002437.5	c.462-18_*60del		splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant	8/8	ENST00000380044.6
MPV17	XM_005264326.5	c.462-18_*60del		splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant	8/8
MPV17	XM_017004151.2	c.414-18_*60del		splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPV17	ENST00000380044.6	c.462-18_*60del		splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant	8/8	1	NM_002437.5	P1

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2023

MPV17: PVS1, PM2 -

Computational scores

Source: dbNSFP v4.3

Splicing

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: chr2-27532719;