22-20982372-A-G

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5

The NM_006767.4(LZTR1):​c.1A>G​(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 33)

Consequence

LZTR1
NM_006767.4 start_lost

Scores

2
3
11

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:1

Conservation

PhyloP100: 0.540
Variant links:
Genes affected
LZTR1 (HGNC:6742): (leucine zipper like post translational regulator 1) This gene encodes a member of the BTB-kelch superfamily. Initially described as a putative transcriptional regulator based on weak homology to members of the basic leucine zipper-like family, the encoded protein subsequently has been shown to localize exclusively to the Golgi network where it may help stabilize the Gogli complex. Deletion of this gene may be associated with DiGeorge syndrome. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

PVS1
Start lost variant, next in-frame start position is after 5 pathogenic variants. Next in-frame start position is after 270 CDS bases. Genomic position: 20985847. Lost 0.107 part of the original CDS.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 22-20982372-A-G is Pathogenic according to our data. Variant chr22-20982372-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1403744.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Pathogenic=1}.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LZTR1NM_006767.4 linkc.1A>G p.Met1? start_lost Exon 1 of 21 ENST00000646124.2 NP_006758.2 Q8N653A0A384NL67

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LZTR1ENST00000646124.2 linkc.1A>G p.Met1? start_lost Exon 1 of 21 NM_006767.4 ENSP00000496779.1 Q8N653

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Hereditary cancer-predisposing syndrome;CN230736:Cardiovascular phenotype Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsJun 25, 2021The p.M1? pathogenic mutation (also known as c.1A>G) is located in coding exon 1 of the LZTR1 gene and results from an A to G substitution at nucleotide position 1. This alters the methionine residue at the initiation codon (ATG). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Sequence variations that modify the initiation codon are expected to result in either loss of translation initiation, N-terminal truncation, or cause a shift in the mRNA reading frame. Based on the supporting evidence, this variant is pathogenic for an increased risk of nerve sheath tumors 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. -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMar 10, 2021The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change affects the initiator methionine of the LZTR1 mRNA. The next in-frame methionine is located at codon 91. This variant has not been reported in the literature in individuals with LZTR1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.0025
T
BayesDel_noAF
Benign
-0.24
CADD
Benign
23
DANN
Uncertain
0.98
DEOGEN2
Benign
0.025
T;T;.
Eigen
Benign
-0.24
Eigen_PC
Benign
-0.14
FATHMM_MKL
Benign
0.31
N
LIST_S2
Uncertain
0.90
.;D;D
M_CAP
Pathogenic
0.50
D
MetaRNN
Pathogenic
0.80
D;D;D
MetaSVM
Benign
-0.95
T
PROVEAN
Benign
-0.060
N;.;.
REVEL
Benign
0.21
Sift
Uncertain
0.027
D;.;.
Sift4G
Benign
0.082
T;.;.
Polyphen
0.015
B;B;.
Vest4
0.55
MutPred
0.85
Loss of glycosylation at P4 (P = 0.0927);Loss of glycosylation at P4 (P = 0.0927);Loss of glycosylation at P4 (P = 0.0927);
MVP
0.13
ClinPred
0.81
D
GERP RS
4.7
RBP_binding_hub_radar
0.97
RBP_regulation_power_radar
2.8
Varity_R
0.55
gMVP
0.47

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-21336661; API