chr12:112488466:C>T Detail (hg38) (PTPN11)

Information

Genome

Assembly Position
hg19 chr12:112,926,270-112,926,270 View the variant detail on this assembly version.
hg38 chr12:112,488,466-112,488,466

HGVS

Type Transcript Protein
RefSeq NM_002834.3:c.1403C>T NP_002825.3:p.Thr468Met
NM_001330437.1:c.1415C>T NP_001317366.1:p.Thr472Met
Ensemble ENST00000351677.7:c.1403C>T ENST00000351677.7:p.Thr468Met
Summary

MGeND

Clinical significance Pathogenic
Variant entry 3
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 176876 OMIM
HGNC 9644 HGNC
Ensembl ENSG00000179295 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv221187371 TogoVar
COSMIC COSM170715 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic colorectal neoplasms, hereditary nonpolyposis somatic MGS000043
(TMGS000096) 		Kohei Miyazono Tokyo University
Pathogenic noonan syndrome germline MGS000083
(TMGS000166) 		Kenjiro Kosaki
Kenjiro Kosaki		 Keio University
Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2023-12-31 criteria provided, single submitter RASopathy germline unknown Detail
Pathogenic 2023-12-22 criteria provided, multiple submitters, no conflicts LEOPARD syndrome 1 germline unknown Detail
Pathogenic Likely pathogenic 2022-02-11 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
Pathogenic 2024-03-17 criteria provided, multiple submitters, no conflicts Noonan syndrome 1 de novo germline unknown Detail
Pathogenic 2022-03-05 criteria provided, multiple submitters, no conflicts Noonan syndrome germline Detail
Pathogenic 2017-04-03 reviewed by expert panel Noonan syndrome with multiple lentigines germline Detail
Pathogenic 2021-10-17 criteria provided, multiple submitters, no conflicts LEOPARD syndrome 1,metachondromatosis,juvenile myelomonocytic leukemia,Noonan syndrome 1 germline unknown Detail
Pathogenic 2021-10-17 criteria provided, multiple submitters, no conflicts LEOPARD syndrome 1,metachondromatosis,juvenile myelomonocytic leukemia,Noonan syndrome 1 germline unknown Detail
Pathogenic 2021-10-17 criteria provided, multiple submitters, no conflicts LEOPARD syndrome 1,metachondromatosis,juvenile myelomonocytic leukemia,Noonan syndrome 1 unknown germline Detail
Pathogenic 2021-10-17 criteria provided, multiple submitters, no conflicts LEOPARD syndrome 1,metachondromatosis,juvenile myelomonocytic leukemia,Noonan syndrome 1 germline unknown Detail
Pathogenic 2018-07-05 no assertion criteria provided PTPN11-related disorder germline Detail
Pathogenic 2017-07-28 criteria provided, single submitter hypertrophic cardiomyopathy germline Detail
Pathogenic 2020-12-21 criteria provided, single submitter Noonan syndrome and Noonan-related syndrome germline Detail
Pathogenic 2022-07-12 criteria provided, single submitter germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.120 Turner Syndrome, Male NA CLINVAR Detail
0.694 Noonan syndrome NA CLINVAR Detail
0.480 LEOPARD Syndrome Furthermore, we show that the recurrent LS-causing Y279C and T468M amino acid su... BeFree 16358218 Detail
0.002 neurofibromatosis 1 LEOPARD syndrome (PTPN11, T468M) in three boys fulfilling neurofibromatosis type... BeFree 21365175 Detail
0.480 LEOPARD Syndrome We report on a family with LEOPARD syndrome which was molecularly proven (p.Thr4... BeFree 17935252 Detail
0.480 LEOPARD Syndrome Here we present a patient with severe, progressive neonatal HCM, elevated urinar... BeFree 22585553 Detail
0.480 LEOPARD Syndrome Diverse driving forces underlie the invariant occurrence of the T42A, E139D, I28... BeFree 18372317 Detail
<0.001 Cardiomyopathies Here we present a patient with severe, progressive neonatal HCM, elevated urinar... BeFree 22585553 Detail
0.480 LEOPARD Syndrome LEOPARD syndrome (PTPN11, T468M) in three boys fulfilling neurofibromatosis type... BeFree 21365175 Detail
0.003 LEOPARD Syndrome Here we present a patient with severe, progressive neonatal HCM, elevated urinar... BeFree 22585553 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND RASopathy ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND LEOPARD syndrome 1 ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND not provided ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND Noonan syndrome 1 ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND Noonan syndrome ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND Noonan syndrome with multiple lentigines ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND multiple conditions ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND multiple conditions ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND multiple conditions ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND multiple conditions ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND PTPN11-related disorder ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND Hypertrophic cardiomyopathy ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND Noonan syndrome and Noonan-related syndrome ClinVar Detail
NM_002834.5(PTPN11):c.1403C>T (p.Thr468Met) AND Cardiovascular phenotype ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
Furthermore, we show that the recurrent LS-causing Y279C and T468M amino acid substitutions engender... DisGeNET Detail
LEOPARD syndrome (PTPN11, T468M) in three boys fulfilling neurofibromatosis type 1 clinical criteria... DisGeNET Detail
We report on a family with LEOPARD syndrome which was molecularly proven (p.Thr468Met in PTPN11) in ... DisGeNET Detail
Here we present a patient with severe, progressive neonatal HCM, elevated urinary catecholamine meta... DisGeNET Detail
Diverse driving forces underlie the invariant occurrence of the T42A, E139D, I282V and T468M SHP2 am... DisGeNET Detail
Here we present a patient with severe, progressive neonatal HCM, elevated urinary catecholamine meta... DisGeNET Detail
LEOPARD syndrome (PTPN11, T468M) in three boys fulfilling neurofibromatosis type 1 clinical criteria... DisGeNET Detail
Here we present a patient with severe, progressive neonatal HCM, elevated urinary catecholamine meta... 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
rs121918457 dbSNP
Genome
hg38
Position
chr12:112,488,466-112,488,466
Variant Type
snv
Reference Allele
C
Alternative Allele
T
East Asian Chromosome Counts (ExAC)
8654
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)
121412
Allele Counts in All Race (ExAC)
1
Heterozygous Counts in All Race (ExAC)
1
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
8.236418146476461E-6
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