rs118161496

Positions:

• chr14-31850092-T-C

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3 BS2

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:
  • Genomes: 𝑓 0.0034 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0038 (19 hom.)
• Consequence: NUBPL NM_025152.3 intron
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:8 U:5
• Conservation: PhyloP100: 3.77

Genes affected

NUBPL (HGNC:20278): (NUBP iron-sulfur cluster assembly factor, mitochondrial) This gene encodes a member of the Mrp/NBP35 ATP-binding proteins family. The encoded protein is required for the assembly of the respiratory chain NADH dehydrogenase (complex I), an oligomeric enzymatic complex located in the inner mitochondrial membrane. Mutations in this gene cause mitochondrial complex I deficiency. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUBPL	NM_025152.3	c.815-27T>C		intron_variant		ENST00000281081.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUBPL	ENST00000281081.12	c.815-27T>C		intron_variant		1	NM_025152.3	P1

Frequencies

GnomAD3 genomes AF: 0.00340 AC: 517 AN: 152256 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.000579

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00131

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.0149

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00444

Gnomad OTH AF: 0.00191

GnomAD3 exomes AF: 0.00345 AC: 857 AN: 248676 Hom.: 10 AF XY: 0.00349 AC XY: 471 AN XY: 134910

Gnomad AFR exome AF: 0.000777

Gnomad AMR exome AF: 0.000726

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000950

Gnomad FIN exome AF: 0.0122

Gnomad NFE exome AF: 0.00442

Gnomad OTH exome AF: 0.00513

GnomAD4 exome AF: 0.00377 AC: 5351 AN: 1419504 Hom.: 19 Cov.: 25 AF XY: 0.00373 AC XY: 2645 AN XY: 709074

Gnomad4 AFR exome AF: 0.000459

Gnomad4 AMR exome AF: 0.000806

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00108

Gnomad4 FIN exome AF: 0.0124

Gnomad4 NFE exome AF: 0.00407

Gnomad4 OTH exome AF: 0.00286

GnomAD4 genome AF: 0.00339 AC: 516 AN: 152374 Hom.: 3 Cov.: 32 AF XY: 0.00364 AC XY: 271 AN XY: 74508

Gnomad4 AFR AF: 0.000577

Gnomad4 AMR AF: 0.00131

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.0149

Gnomad4 NFE AF: 0.00442

Gnomad4 OTH AF: 0.00189

Alfa AF: 0.00323 Hom.: 0

Bravo AF: 0.00228

Asia WGS AF: 0.000289 AC: 1 AN: 3476

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:8 Uncertain:5

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Mitochondrial complex 1 deficiency, nuclear type 21 Pathogenic:5 Uncertain:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Jul 20, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 07, 2023	Variant summary: NUBPL c.815-27T>C is located at a position not widely known to affect splicing. 4/4 computational tools predict no significant impact on normal splicing. However, at least two publications report experimental evidence that this variant affects mRNA splicing (Tucker_2012, Kimonis_2021). The variant allele was found at a frequency of 0.0034 in 248676 control chromosomes in the gnomAD database, including 10 homozygotes. 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, Kimonis_2021), and some were reported as compound heterozygous with other (likely) pathogenic variants. These data indicate that the variant is very likely to 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). 11 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and classified it as pathogenic/likely pathogenic (n=8) or uncertain significance (n=3). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital	Jun 15, 2018	[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]. -
Uncertain significance, criteria provided, single submitter	clinical testing	Undiagnosed Diseases Network, NIH	Aug 24, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Oct 19, 2020	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 -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jan 08, 2024	- -

not provided Pathogenic:1 Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2023	NUBPL: PM3:Strong, PS3:Moderate, PM2:Supporting, PP3, BS2 -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 14, 2017	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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Jan 09, 2017	- -

Mitochondrial complex I deficiency Pathogenic:1 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 16, 2024	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	May 01, 2017	- -

Inborn genetic diseases Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 13, 2021

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	22
DANN	Benign	0.68
BranchPoint Hunter		6.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.71		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.70		Position offset: -45
DS_AL_spliceai		0.71		Position offset: 27

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

Publications

LitVar

Other links and lift over

dbSNP: rs118161496; hg19: chr14-32319298;