rs118161496
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_025152.3(NUBPL):c.815-27T>C variant causes a intron change. The variant allele was found at a frequency of 0.00373 in 1,571,878 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_025152.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.00340 AC: 517AN: 152256Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00345 AC: 857AN: 248676Hom.: 10 AF XY: 0.00349 AC XY: 471AN XY: 134910
GnomAD4 exome AF: 0.00377 AC: 5351AN: 1419504Hom.: 19 Cov.: 25 AF XY: 0.00373 AC XY: 2645AN XY: 709074
GnomAD4 genome 0.00339 AC: 516AN: 152374Hom.: 3 Cov.: 32 AF XY: 0.00364 AC XY: 271AN XY: 74508
ClinVar
Submissions by phenotype
Mitochondrial complex 1 deficiency, nuclear type 21 Pathogenic:4Uncertain:2
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[ACMG/AMP: PS3, PP3, PP5, BS1] This alteration is supported by well-established in vitro or in vivo functional studies to have a damaging effect on protein function or splicing [PS3], is predicted to be damaging by multiple functional prediction tools [PP3], was reported as a pathogenic/likely pathogenic alteration by a reputable source (ClinVar or other correspondence from a clinical testing laboratory) [PP5], has an allele frequency that is greater than expected for the associated disease [BS1]. -
Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as 3B-VUS. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0106 - This gene is known to be associated with autosomal recessive disease. (N) 0210 - Splice site variant (canonical or non-canonical) proven to affect splicing/expression of the transcript with a known effect on protein structure. Functional studies showed three alternate transcripts were generated as a result of aberrant splicing from the allele with this variant: one transcript with normal splicing, one with exon 10 skipped resulting in a frameshift but no nonsense-mediated decay (NMD), and a third transcript that utilised a cryptic splice site resulting in a frameshift and NMD (PMIDs: 22072591, 32518176). (P) 0251 - Variant is heterozygous. (N) 0305 - Variant is present in gnomAD >=0.01 and <0.03 for a recessive condition (972 heterozygotes, 10 homozygotes). (N) 0705 - No comparable variants have previous evidence for pathogenicity. (N) 0803 - Low previous evidence of pathogenicity in unrelated individuals. An allele harbouring this variant in cis with a second variant (p.(Gly56Arg)) has been reported as pathogenic in many patients, majority of whom were in compound heterozygous state with a pathogenic allele (PMIDs: 22072591, 25245479, 23553477). However, an allele harbouring this variant without the p.(Gly56Arg) variant has been associated with disease in one family (PMID: 32518176). (P) 1001 - Strong functional evidence supporting abnormal protein function. Functional studies showed levels of NUBPL mRNA and protein were decreased in the fibroblast cells heterozygous for this variant alone (PMID: 22072591). (P) 1205 - Variant is maternally inherited. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign -
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not provided Pathogenic:2Uncertain:2
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PP1, PP3, PM3, PS3 -
NUBPL: PM3:Strong, PS3:Moderate, PM2:Supporting, PP3, BS2 -
Expression studies of the c.815-27 T>C sequence change found that this variant impairs mRNA splicing resulting in a 80% decrease in complex I assembly and function (Tucker et al., 2012; Wydro et al., 2013). Therefore, based on the currently available information, the c.815-27 T>C variant is a strong candidate for a pathogenic variant; however, the possibility that it is a benign variant cannot be excluded. -
Inborn genetic diseases Pathogenic:1
The c.815-27T>C intronic alteration consists of a T to C substitution 27 nucleotides before coding exon 10 in the NUBPL gene and is predicted to affect the native branch site. Based on data from the Genome Aggregation Database (gnomAD) database, the NUBPL c.815-27T>C alteration was observed in 0.35% (992/280082) of total alleles studied (including 10 homozygotes), with a frequency of 1.24% (310/24978) in the European (Finnish) subpopulation. The [c.166G>A (p.G56R); c.815-27T>C] complex allele has been reported in the homozygous state, compound heterozygous state, and confirmed in trans with a second pathogenic allele in multiple unrelated patients with mitochondrial encephalomyopathy (Calvo, 2010; Kevelam, 2013). Emerging evidence is suggestive that the NUBPL [c.166G>A (p.G56R); c.815-27T>C] complex allele is likely pathogenic when these alterations are in cis; however, the clinical significance of these alterations in isolation remains uncertain. The c.815-27T nucleotide is highly conserved in available vertebrate species. Functional analysis of cultured fibroblasts from a patient bearing the [c.166G>A (p.G56R); c.815-27T>C] complex allele in trans with a complex rearrangement, as well as a control patient who was heterozygous for only the c.815-27T>C alteration, demonstrated an aberrant RT-PCR pattern with three distinct transcripts: wild-type, a lengthened transcript resulting from a cryptic splice site which introduces an additional 72 bp and results in a frameshift (p.G272Vfs*11), as well as a truncated transcript generated due to exon 10 skipping resulting in a frameshift (p.D273Qfs*31) (Tucker, 2012). Analysis by qRT-PCR and Western blot showed that the heterozygous control with only the c.815-27T>C alteration had reduced mRNA expression (74%) and protein expression (59%) compared to wild type controls, and the patient with the [c.166G>A (p.G56R); c.815-27T>C] complex allele and complex rearrangement on the other allele had more significant reduction in mRNA expression (15%) and undetectable protein expression (Tucker, 2012). No defective function was identified when the protein with the G56R missense change was over-expressed (Tucker, 2012). The p.D273Qfs*31 transcript is completely non-functional in yeast assays (Wydro, 2013; Maclean, 2018). In silico splice site analysis predicts that the c.815-27T>C alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. Based on the available evidence, this alteration is classified as likely pathogenic. -
not specified Uncertain:1
Variant summary: NUBPL c.815-27T>C is located at a position not widely known to affect splicing. Consensus agreement among computation tools predict no significant impact on normal splicing. At least one publication reports experimental evidence that this variant affects mRNA splicing (Tucker_2012, Kimonis_2021, Calvo_2010). The variant allele was found at a frequency of 0.0037 in 1571878 control chromosomes in the gnomAD database (v4), including 22 homozygotes. The observed variant frequency exceeds the estimated maximal expected allele frequency for a pathogenic variant in NUBPL causing Mitochondrial Complex 1 Deficiency, Nuclear Type 21 phenotype. c.815-27T>C has been reported in the literature in multiple individuals affected with Mitochondrial Complex 1 Deficiency, Nuclear Type 21 (Calvo_2010, Kevelam_2013, Haskell_2018, Maclean_2018, Kimonis_2021), however it is usually observed in cis with the c.166G>A (p.G56R) variant. These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein expression, finding that a heterozygous control with the variant exhibited far lower expression of NUBPL protein (Tucker_2012). The following publications have been ascertained in the context of this evaluation (PMID: 20818383, 23553477, 22072591, 32518176, 29982452, 29417091). ClinVar contains an entry for this variant (Variation ID: 50317). There is not enough evidence at this time to determine if this variant is associated with disease in isolation. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -
Mitochondrial complex I deficiency Uncertain:1
The c.815-27T>C variant in NUBPL is typically observed as a compound allele (in cis) with the c.166G>A [p.G56R] variant in individuals with mitochondrial complex I deficiency. By itself, it has been reported in at least one individual with mitochondrial complex I deficiency and an another variant in trans, and segregated with disease in at least 1 sibling (Kimonis 2021 PMID: 32518176; Maclean 2018 PMID:29982452). This variant has also been identified in 1.28% (819/63974) of European (Finnish) chromosomes, including 22 homozygotes, by gnomAD (http://gnomad.broadinstitute.org, v4.0.0) and reported in ClinVar (Variation ID 50317). This variant is located in the splice branch site, and computational prediction tools suggest an impact on splicing. An RT-PCR study demonstrated that this variant results in three transcripts: wild-type, the use of a cryptic acceptor site (p.G272VfsX11), or skipping of exon 10 (p.D273QfsX31). In addition, in vitro functional studies demonstrated that patient cells express reduced levels of the wild-type transcript, possibly as a result of degradation of a variant transcript by NMD (Tucker 2012 PMID: 22072591). Overall, it is unclear if this variant in isolation causes disease or whether it acts in synergy with the p.G56R variant. Therefore, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM3, PP1, PP3, PS3_Supporting, BS1_Supporting. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at