19-5679642-CG-C

Variant names:

• chr19-5679642-CG-C
• rs751944867
• NM_205767.3:c.150delC

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_205767.3(MICOS13):​c.150delC​(p.Ala51ProfsTer39) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,458,530 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: MICOS13 NM_205767.3 frameshift
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:1
• Conservation: PhyloP100: -6.75

Genes affected

MICOS13 (HGNC:33702): (mitochondrial contact site and cristae organizing system subunit 13) Involved in cristae formation. Located in mitochondrial crista junction and nucleoplasm. Part of MICOS complex. Implicated in combined oxidative phosphorylation deficiency 37. [provided by Alliance of Genome Resources, Apr 2022]

RPL36 (HGNC:13631): (ribosomal protein L36) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L36E family of ribosomal proteins. It is located in the cytoplasm. Transcript variants derived from alternative splicing exist; they encode the same protein. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 11 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 19-5679642-CG-C is Pathogenic according to our data. Variant chr19-5679642-CG-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1526386.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICOS13	NM_205767.3	c.150delC	p.Ala51ProfsTer39	frameshift_variant	Exon 2 of 4	ENST00000309324.9	NP_991330.1
MICOS13	NM_001308240.2	c.216delC	p.Ala73ProfsTer39	frameshift_variant	Exon 3 of 5		NP_001295169.1
MICOS13	NM_001365761.2	c.216delC	p.Ala73ProfsTer39	frameshift_variant	Exon 2 of 4		NP_001352690.1
MICOS13	XM_011527675.3	c.216delC	p.Ala73ProfsTer59	frameshift_variant	Exon 2 of 4		XP_011525977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICOS13	ENST00000309324.9	c.150delC	p.Ala51ProfsTer39	frameshift_variant	Exon 2 of 4	1	NM_205767.3	ENSP00000309561.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1458530 Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2 AN XY: 725620

Gnomad4 AFR exome AF: 0.0000599

Gnomad4 AMR exome AF: 0.0000227

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.00e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1

Feb 09, 2024

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Frameshift variant predicted to result in abnormal protein length as the last 68 amino acids are replaced with 38 different amino acids, and other similar variants have been reported in HGMD; Has not been previously published as pathogenic or benign to our knowledge -

Combined oxidative phosphorylation deficiency 37 Uncertain:1

-

Royal Medical Services, Bahrain Defence Force Hospital

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The MICOS13 variant c.150del p.(Ala51Profs*39) creates a shift in the reading frame starting at codon 51 in exon(s) no. 2 (of 4). To the best of our knowledge this is a novel variant not previously reported in the literature. ClinVar lists this variant (Interpretation: Likely pathogenic; Variation ID: 1526386). It is classified as variant of uncertain significance based on the ACMG/AMP/ClinGen SVI guidelines. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs751944867; hg19: chr19-5679653;