rs587777176
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PP5_Very_Strong
The NM_006767.4(LZTR1):c.264-13G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,613,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_006767.4 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LZTR1 | NM_006767.4 | c.264-13G>A | intron_variant | Intron 2 of 20 | ENST00000646124.2 | NP_006758.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251194Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135866
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461664Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727148
GnomAD4 genome AF: 0.000158 AC: 24AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74324
ClinVar
Submissions by phenotype
LZTR1-related schwannomatosis Pathogenic:4
- -
- -
PS3_Very Strong -
- -
not provided Pathogenic:4
Non-canonical splice site variant demonstrated to result in loss of function (PMID: 24362817); Identified in patients with schwannomatosis in published literature and referred for genetic testing at GeneDx (PMID: 24362817, 31128261, 29409008); This variant is associated with the following publications: (PMID: 24362817, 31128261, 29409008, 31438995, 34426522, 27921248, 36495689) -
- -
LZTR1: PS3:Moderate, PS4:Moderate, PM2:Supporting, PP1, PP3 -
This sequence change falls in intron 2 of the LZTR1 gene. It does not directly change the encoded amino acid sequence of the LZTR1 protein. This variant is present in population databases (rs587777176, gnomAD 0.02%). This variant has been observed in individuals with schwannomatosis (PMID: 24362817, 31128261, 31438995). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 101034). Studies have shown that this variant is associated with altered splicing resulting in inclusion of intronic sequence (PMID: 24362817). For these reasons, this variant has been classified as Pathogenic. -
Noonan syndrome 2 Pathogenic:2
PM2_Supporting+PS3+PM3 -
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with autosomal recessive Noonan syndrome 2 (MIM#605275). Dominant negative is the mechanism suspected for autosomal dominant Noonan syndrome 10 (MIM#616564). (I) 0108 - This gene is associated with both recessive and dominant disease. (I) 0210 - Splice site variant proven to affect splicing of the transcript with a known effect on protein sequence. RT-PCR studies have demonstrated that this variant creates a cryptic splice acceptor site, leading to the retention of 11 intronic nucleotides and creating a frameshift (p. (Lys89Cysfs*16) that is expected to undergo nonsense-mediated decay (NMD) (PMID:24362817). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (24 heterozygotes, 0 homozygotes). (SP) 0701 - Other NMD predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. There are many of these variants reported as pathogenic in ClinVar. (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported eight times in ClinVar as pathogenic, once as likely pathogenic and once as a variant of unknown significance. (SP) 1206 - This variant has been shown to be paternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Hereditary cancer-predisposing syndrome;CN230736:Cardiovascular phenotype Pathogenic:1
The c.264-13G>A intronic pathogenic mutation results from a G to A substitution 13 nucleotides upstream from coding exon 3 in the LZTR1 gene. This alteration has been identified in multiple individuals diagnosed with schwannomatosis and has been reported to segregate with disease in one family (Piotrowski A et al. Nat. Genet., 2014 Feb;46:182-7; Louvrier C et al. Neuro-oncology, 2018 06;20:917-929; Deiller C et al. Eur J Med Genet, 2019 Aug;62:103680). In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. RNA studies confirm that the predicted alternate splice acceptor site is utilized, resulting in the inclusion of 11 intronic nucleotides at the beginning of coding exon 3 and a frameshift (r.263_264ins264-11_264-1 p.K89Cfs*16) (Piotrowski A et al. Nat. Genet., 2014 Feb;46:182-7; Ambry internal data). This nucleotide position is not well conserved in available vertebrate species. Based on the supporting evidence, this variant is pathogenic for an increased risk of LZTR1-related schwannomatosis (SWN) and would be expected to cause autosomal recessive Noonan syndrome when present along with a second pathogenic or likely pathogenic variant on the other allele; however, the association of this alteration with autosomal dominant Noonan syndrome is unlikely. -
Schwannomatosis Pathogenic:1
Variant summary: LZTR1 c.264-13G>A alters a non-conserved nucleotide located at a position not widely known to affect splicing. Several computational tools predict a significant impact on normal splicing: One predict the variant abolishes a 3 acceptor site. Two predict the variant weakens a 3' acceptor site. Five predict the variant creates a 3' acceptor site. At least one publication reports experimental evidence that this variant affects mRNA splicing (Piotrowski_2014). The variant allele was found at a frequency of 4.4e-05 in 251194 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in LZTR1 related diseases. c.264-13G>A has been reported in the literature in multiple individuals affected with Schwannomatosis (Piotrowski_2014, Alaidarous_2019, Deiller_2019, Louvrier_2018). These data indicate that the variant is very likely to be associated with disease. To our knowledge, this variant has not been reported in patients with Noonan Syndrome. The following publications have been ascertained in the context of this evaluation (PMID: 24362817, 29409008, 27921248, 31438995, 31128261). ClinVar contains an entry for this variant (Variation ID: 101034). Based on the evidence outlined above, the variant was classified as pathogenic. -
Noonan syndrome 2;C3810283:LZTR1-related schwannomatosis;C4225280:Noonan syndrome 10 Pathogenic:1
- -
Developmental disorder Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at