21-25599860-GA-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_017446.4(MRPL39):c.526del(p.Ser176LeufsTer8) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000263 in 1,613,072 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00028 ( 0 hom. )
Consequence
MRPL39
NM_017446.4 frameshift
NM_017446.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.971
Genes affected
MRPL39 (HGNC:14027): (mitochondrial ribosomal protein L39) Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein. Two transcript variants encoding distinct isoforms have been described. A pseudogene corresponding to this gene is found on chromosome 5q. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
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Very rare variant in population databases, with high coverage;
PP5
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Variant 21-25599860-GA-G is Pathogenic according to our data. Variant chr21-25599860-GA-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1676673.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPL39 | NM_017446.4 | c.526del | p.Ser176LeufsTer8 | frameshift_variant | 5/10 | ENST00000352957.9 | |
MRPL39 | NM_080794.4 | c.526del | p.Ser176LeufsTer8 | frameshift_variant | 5/11 | ||
MRPL39 | XM_006724026.5 | c.526del | p.Ser176LeufsTer8 | frameshift_variant | 5/10 | ||
MRPL39 | XM_011529651.3 | c.400del | p.Ser134LeufsTer8 | frameshift_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL39 | ENST00000352957.9 | c.526del | p.Ser176LeufsTer8 | frameshift_variant | 5/10 | 1 | NM_017446.4 | P1 | |
MRPL39 | ENST00000307301.11 | c.526del | p.Ser176LeufsTer8 | frameshift_variant | 5/11 | 5 | |||
MRPL39 | ENST00000419219.1 | c.521-25del | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152156Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000997 AC: 25AN: 250694Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135554
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GnomAD4 exome AF: 0.000277 AC: 405AN: 1460916Hom.: 0 Cov.: 30 AF XY: 0.000268 AC XY: 195AN XY: 726812
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Leigh syndrome Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Jun 24, 2022 | Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Likely Pathogenic. Following criteria are met: 0102 - Loss of function is a suggested mechanism of disease in this gene and is associated with lethal infantile mitochondrial disease. (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 30 heterozygotes, 0 homozygotes). (SP) 0402 - Variant is located in a gene associated with a severe early-onset recessive condition that is intolerant to bi-allelic loss of function variants (gnomAD). (SP) 0703 - Other NMD-predicted variants comparable to the one identified in this case have moderate previous evidence for pathogenicity. (SP) 0807 - This variant has no previous evidence of pathogenicity. (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1001 - This variant has strong functional evidence supporting abnormal protein function. Western blots on patient fibroblasts showed destabilisation of the mitoribosome and defective translation of the OXPHOS complexes. (SP) 1206 - This variant has been shown to be paternally inherited. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign - |
Pathogenic, no assertion criteria provided | research | Mitochondrial Research Group, Murdoch Children's Research Institute | Apr 03, 2022 | - - |
Combined oxidative phosphorylation deficiency 59 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 04, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at