Variant Detail

Variant Information
ID
DPV: 6930
Chromosome
10
Gene
HGVS (GRCh37/hg19)
NC_000010.10:g.89692905G>A
HGVS (GRCh38/hg38)
NC_000010.11:g.87933148G>A
HGVS (RNA)
NM_000314.6:c.389G>A
HGVS (Protein)
NP_000305.3:p.R130Q
dbSNP
-
ClinGen Allele Registry
CA000437
Allele Frequency
Individual Information

ID
DPVS:7486.1
Clinical Significance
Pathogenic
Date Last Evaluated
2019-03-28
Clinical Significance Citation
Nyuzuki, H. PTEN mutation in a Japanese boy with autonomously functioning thyroid nodule. 2017 Pediatr Int. 2017 Nov;59(11):1223-1224. doi: 10.1111/ped.13427. PMID:29359449

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
-

ClinVar
Model Animals
VCF
VCF (GRCh37/hg19) 
											##fileformat=VCFv4.0
##reference=GRCh37
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=EXAC_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ExAC r1)">
##INFO=<ID=EXAC_FILTER,Number=1,Type=String,Description="calculated by self of overlapping values in field FILTER (from ExAC r1)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=HGVD_AAF,Number=A,Type=Float,Description="Alternative Allele Frequency(s) NA/(NR+NAtotal) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_AC,Number=A,Type=Integer,Description="number(s) of alternative allele(s) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_NR,Number=1,Type=Integer,Description="number of reference allele (from HGVD/DBexome20170802)">
##INFO=<ID=TOMMO_4_7K_AC,Number=A,Type=Integer,Description="Allele count in genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed  (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
10	89692905	NC_000010.10:g.89692905G>A	G	A	.	.	CLNALLELEID=22868;CLNDN=Neoplasm|Breast_neoplasm|Renal_cell_carcinoma,_papillary,_1|Malignant_melanoma_of_skin|Small_cell_lung_carcinoma|Squamous_cell_lung_carcinoma|Neoplasm_of_ovary|Neoplasm_of_the_large_intestine|Adenocarcinoma_of_stomach|Adenocarcinoma_of_prostate|Uterine_Carcinosarcoma|Cowden_syndrome_1|Squamous_cell_carcinoma_of_the_head_and_neck|Hereditary_cancer-predisposing_syndrome|PTEN_hamartoma_tumor_syndrome|Glioblastoma|Neoplasm_of_uterine_cervix|Malignant_neoplasm_of_body_of_uterus|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0002664,Human_Phenotype_Ontology:HP:0003008,Human_Phenotype_Ontology:HP:0006741,MeSH:D009369,MedGen:C0027651,SNOMED_CT:108369006|Human_Phenotype_Ontology:HP:0010623,Human_Phenotype_Ontology:HP:0100013,MONDO:MONDO:0021100,MeSH:D001943,MedGen:C1458155,SNOMED_CT:126926005|Human_Phenotype_Ontology:HP:0011797,MedGen:C1336839,OMIM:605074|Human_Phenotype_Ontology:HP:0012056,MONDO:MONDO:0005012,MeSH:C562393,MedGen:C0151779,SNOMED_CT:93655004|Human_Phenotype_Ontology:HP:0030357,MONDO:MONDO:0008433,MeSH:D055752,MedGen:C0149925,OMIM:182280,Orphanet:ORPHA70573|Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|Human_Phenotype_Ontology:HP:0100615,MONDO:MONDO:0021068,MeSH:D010051,MedGen:C0919267,OMIM:167000,SNOMED_CT:123843001|Human_Phenotype_Ontology:HP:0100834,MeSH:D015179,MedGen:C0009404,SNOMED_CT:126837005|MONDO:MONDO:0005036,MedGen:C0278701|MONDO:MONDO:0005082,MedGen:C0007112|MONDO:MONDO:0006485,MedGen:C0280630|MONDO:MONDO:0008021,MedGen:CN072330,OMIM:158350|MONDO:MONDO:0010150,MeSH:D000077195,MedGen:C1168401,OMIM:275355,SNOMED_CT:716659002|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0017623,MedGen:C1959582,OMIM:601728,Orphanet:ORPHA306498|MONDO:MONDO:0018177,MeSH:D005909,MedGen:C0017636,Orphanet:ORPHA360,SNOMED_CT:63634009|MONDO:MONDO:0021230,MeSH:D002583,MedGen:C0007873,SNOMED_CT:123841004|MedGen:C0153574|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000010.10:g.89692905G>A;GENEINFO=9588:5728;DPVID=6930;DPVSIG=Pathogenic;DPVDSDBID=OMIM:158350;DPVDBN=Lhermitte-Duclos_disease;DPVHGVS=NC_000010.10:g.89692905G>A	.
VCF (GRCh38/hg38) 
											##fileformat=VCFv4.0
##reference=GRCh38
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##originalFile=</tmp/crossmap-input-0we2er1k>
##targetRefGenome=</usr/lib64/python2.7/site-packages/transvar/transvar.download/hg38.fa>
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
10	87933148	NC_000010.10:g.89692905G>A	G	A	.	.	dbSNP_RSID=rs121909229;CLNALLELEID=22868;CLNDN=Neoplasm|Breast_neoplasm|Renal_cell_carcinoma,_papillary,_1|Malignant_melanoma_of_skin|Small_cell_lung_carcinoma|Squamous_cell_lung_carcinoma|Neoplasm_of_ovary|Neoplasm_of_the_large_intestine|Adenocarcinoma_of_stomach|Adenocarcinoma_of_prostate|Uterine_Carcinosarcoma|Cowden_syndrome_1|Squamous_cell_carcinoma_of_the_head_and_neck|Hereditary_cancer-predisposing_syndrome|PTEN_hamartoma_tumor_syndrome|Glioblastoma|Neoplasm_of_uterine_cervix|Malignant_neoplasm_of_body_of_uterus|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0002664,Human_Phenotype_Ontology:HP:0003008,Human_Phenotype_Ontology:HP:0006741,MeSH:D009369,MedGen:C0027651,SNOMED_CT:108369006|Human_Phenotype_Ontology:HP:0010623,Human_Phenotype_Ontology:HP:0100013,MONDO:MONDO:0021100,MeSH:D001943,MedGen:C1458155,SNOMED_CT:126926005|Human_Phenotype_Ontology:HP:0011797,MeSH:D002292,MedGen:C1336839,OMIM:605074|Human_Phenotype_Ontology:HP:0012056,MONDO:MONDO:0005012,MeSH:C562393,MedGen:C0151779,OMIM:PS155600,SNOMED_CT:93655004|Human_Phenotype_Ontology:HP:0030357,MONDO:MONDO:0008433,MeSH:D055752,MedGen:C0149925,OMIM:182280,Orphanet:ORPHA70573|Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|Human_Phenotype_Ontology:HP:0100615,MONDO:MONDO:0021068,MeSH:D010051,MedGen:C0919267,OMIM:167000,SNOMED_CT:123843001|Human_Phenotype_Ontology:HP:0100834,MeSH:D015179,MedGen:C0009404,SNOMED_CT:126837005|MONDO:MONDO:0005036,MedGen:C0278701|MONDO:MONDO:0005082,MedGen:C0007112|MONDO:MONDO:0006485,MedGen:C0280630|MONDO:MONDO:0008021,MedGen:CN072330,OMIM:158350|MONDO:MONDO:0010150,MeSH:C535575,MedGen:C1168401,OMIM:275355,Orphanet:ORPHA67037,SNOMED_CT:_716659002|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0017623,MedGen:C1959582,OMIM:601728,Orphanet:ORPHA306498|MONDO:MONDO:0018177,MeSH:D005909,MedGen:C0017636,Orphanet:ORPHA360,SNOMED_CT:63634009|MeSH:D002583,MedGen:C0007873,SNOMED_CT:123841004|MedGen:C0153574|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000010.11:g.87933148G>A;GENEINFO=9588:5728;DPVID=6930;DPVSIG=Pathogenic;DPVDSDBID=OMIM:158350;DPVDBN=Lhermitte-Duclos_disease;DPVHGVS=NC_000010.11:g.87933148G>A	.