chr22:21348256:G>A Detail (hg19) (LZTR1)

Information

Genome

Assembly Position
hg19 chr22:21,348,256-21,348,256
hg38 chr22:20,993,967-20,993,967 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000646124.2:c.1397G>A ENST00000646124.2:p.Arg466Gln
ENST00000700578.1:c.1397G>A ENST00000700578.1:p.Arg466Gln
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Likely pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 600574 OMIM
HGNC 6742 HGNC
Ensembl ENSG00000099949 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv65422557 TogoVar
COSMIC COSM3972870 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely pathogenic 2023-06-23 criteria provided, single submitter schwannomatosis 2 unknown Detail
Likely pathogenic 2020-09-16 criteria provided, single submitter schwannomatosis germline Detail
Likely pathogenic 2024-01-21 criteria provided, multiple submitters, no conflicts not provided germline Detail
Likely pathogenic 2021-03-31 criteria provided, single submitter Noonan syndrome and Noonan-related syndrome germline Detail
Likely pathogenic 2023-03-08 criteria provided, single submitter Hereditary cancer-predisposing syndrome germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.240 schwannomatosis 2 NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_006767.4(LZTR1):c.1397G>A (p.Arg466Gln) AND Schwannomatosis 2 ClinVar Detail
NM_006767.4(LZTR1):c.1397G>A (p.Arg466Gln) AND Schwannomatosis ClinVar Detail
NM_006767.4(LZTR1):c.1397G>A (p.Arg466Gln) AND not provided ClinVar Detail
NM_006767.4(LZTR1):c.1397G>A (p.Arg466Gln) AND Noonan syndrome and Noonan-related syndrome ClinVar Detail
NM_006767.4(LZTR1):c.1397G>A (p.Arg466Gln) AND multiple conditions ClinVar Detail
NA DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs587777180 dbSNP
Genome
hg19
Position
chr22:21,348,256-21,348,256
Variant Type
snv
Reference Allele
G
Alternative Allele
A
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs587777180
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0002
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
7698
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
105626
Allele Counts in All Race (ExAC)
4
Heterozygous Counts in All Race (ExAC)
4
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
3.786946395773768E-5
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