Variant Detail

Variant Information
ID
DPV: 12097
Chromosome
3
Gene
HGVS (GRCh37/hg19)
NC_000003.11:g.178952084C>T
HGVS (GRCh38/hg38)
NC_000003.12:g.179234296C>T
HGVS (RNA)
NM_006218.2:c.3139C>T
HGVS (Protein)
NP_006209.2:p.H1047Y
dbSNP
-
ClinGen Allele Registry
CA130471
Allele Frequency
Individual Information

ID
DPVS:13264.2
Clinical Significance
Pathogenic
Date Last Evaluated
2020-07-03
Clinical Significance Citation
Trani, A. Carboxyhydrazides of the aglycone of teicoplanin. Synthesis and antibacterial activity. 1990 J Antibiot (Tokyo). 1990 Nov;43(11):1471-82. doi: 10.7164/antibiotics.43.1471. PMID:2272922

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
de novo
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing
Collection Method
clinical testing
Compound heterozygous variant(s)
Data Submitter
Comment
sample:Right nail|mosaic|This variant was detected in  IRUD (Initiative on Rare and Undiagnosed Diseases) project.

ClinVar
Model Animals
VCF
VCF (GRCh37/hg19) 
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##reference=GRCh37
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##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
3	178952084	NC_000003.11:g.178952084C>T	C	T	.	.	CLNALLELEID=48304;CLNDN=Hepatocellular_carcinoma|Medulloblastoma|Adrenocortical_carcinoma|Congenital_macrodactylia|Pancreatic_adenocarcinoma|Transitional_cell_carcinoma_of_the_bladder|Neoplasm_of_stomach|Breast_neoplasm|Brainstem_glioma|Epidermal_nevus|Carcinoma_of_esophagus|Renal_cell_carcinoma,_papillary,_1|Malignant_melanoma_of_skin|Lung_adenocarcinoma|Non-small_cell_lung_cancer|Squamous_cell_lung_carcinoma|Neoplasm_of_brain|Seborrheic_keratosis|Neoplasm_of_ovary|Neoplasm_of_the_large_intestine|Carcinoma_of_colon|Adenocarcinoma_of_stomach|Adenocarcinoma_of_prostate|Lung_carcinoma|Ovarian_Serous_Cystadenocarcinoma|Uterine_Carcinosarcoma|Squamous_cell_carcinoma_of_the_head_and_neck|Megalencephaly-capillary_malformation-polymicrogyria_syndrome|Congenital_lipomatous_overgrowth,_vascular_malformations,_and_epidermal_nevi|Capillary_malformation_of_the_lower_lip,_lymphatic_malformation_of_face_and_neck,_asymmetry_of_face_and_limbs,_and_partial/generalized_overgrowth|Cowden_syndrome_5|Cowden_syndrome|Familial_cancer_of_breast|Glioblastoma|Neoplasm_of_uterine_cervix|Malignant_tumor_of_floor_of_mouth|Malignant_neoplasm_of_body_of_uterus|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0001402,Human_Phenotype_Ontology:HP:0002899,Human_Phenotype_Ontology:HP:0003007,Human_Phenotype_Ontology:HP:0006750,MedGen:C2239176,OMIM:114550,Orphanet:ORPHA88673,SNOMED_CT:187769009,SNOMED_CT:25370001|Human_Phenotype_Ontology:HP:0002885,MONDO:MONDO:0007959,MeSH:D008527,MedGen:C0025149,OMIM:155255,Orphanet:ORPHA616|Human_Phenotype_Ontology:HP:0002889,Human_Phenotype_Ontology:HP:0006744,Human_Phenotype_Ontology:HP:0006759,MONDO:MONDO:0006639,MeSH:D018268,MedGen:C0206686|Human_Phenotype_Ontology:HP:0004099,MONDO:MONDO:0007962,MedGen:C0265552,OMIM:155500,SNOMED_CT:48449000|Human_Phenotype_Ontology:HP:0006725,MONDO:MONDO:0006047,MedGen:C0281361|Human_Phenotype_Ontology:HP:0006740,MONDO:MONDO:0005611,MedGen:C0279680|Human_Phenotype_Ontology:HP:0006753,MONDO:MONDO:0021085,MeSH:D013274,MedGen:C0038356,SNOMED_CT:126824007|Human_Phenotype_Ontology:HP:0010623,Human_Phenotype_Ontology:HP:0100013,MONDO:MONDO:0021100,MeSH:D001943,MedGen:C1458155,SNOMED_CT:126926005|Human_Phenotype_Ontology:HP:0010796,MONDO:MONDO:0002911,MedGen:C0677865|Human_Phenotype_Ontology:HP:0010816,MONDO:MONDO:0008093,MedGen:C0334082,OMIM:162900,SNOMED_CT:25201003|Human_Phenotype_Ontology:HP:0011459,MONDO:MONDO:0019086,MedGen:C0152018,Orphanet:ORPHA70482|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:0030078,MONDO:MONDO:0005061,MeSH:D000077192,MedGen:C0152013|Human_Phenotype_Ontology:HP:0030358,MONDO:MONDO:0005233,MeSH:D002289,MedGen:C0007131,SNOMED_CT:254637007|Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|Human_Phenotype_Ontology:HP:0030692,MONDO:MONDO:0021211,MeSH:D001932,MedGen:C0006118,SNOMED_CT:126952004|Human_Phenotype_Ontology:HP:0031287,MONDO:MONDO:0008420,MedGen:C0022603,OMIM:182000|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:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0005036,MedGen:C0278701|MONDO:MONDO:0005082,MedGen:C0007112|MONDO:MONDO:0005138,MedGen:C0684249|MONDO:MONDO:0006046,MedGen:C0279663|MONDO:MONDO:0006485,MedGen:C0280630|MONDO:MONDO:0010150,MeSH:D000077195,MedGen:C1168401,OMIM:275355,SNOMED_CT:716659002|MONDO:MONDO:0011240,MedGen:C1865285,OMIM:602501,Orphanet:ORPHA60040|MONDO:MONDO:0013038,MedGen:C2752042,OMIM:612918,Orphanet:ORPHA140944|MONDO:MONDO:0013125,MedGen:C2751313,OMIM:613089,Orphanet:ORPHA168984|MONDO:MONDO:0014047,MedGen:C3554518,OMIM:615108|MONDO:MONDO:0016063,MedGen:C0018553,OMIM:PS158350,Orphanet:ORPHA201,SNOMED_CT:58037000|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MONDO:MONDO:0018177,MeSH:D005909,MedGen:C0017636,Orphanet:ORPHA360,SNOMED_CT:63634009|MONDO:MONDO:0021230,MeSH:D002583,MedGen:C0007873,SNOMED_CT:123841004|MONDO:MONDO:0021320,MedGen:C0153368|MedGen:C0153574|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000003.11:g.178952084C>T;GENEINFO=8975:5290;DPVID=12097;DPVSIG=Pathogenic;DPVDSDBID=OMIM:602501;DPVDBN=Megalencephaly-capillary_malformation-polymicrogyria_syndrome;DPVHGVS=NC_000003.11:g.178952084C>T	.
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-_0ozfjtg>
##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
3	179234296	NC_000003.11:g.178952084C>T	C	T	.	.	dbSNP_RSID=rs121913281;CLNALLELEID=48304;CLNDN=Hepatocellular_carcinoma|Medulloblastoma|Adrenocortical_carcinoma|Congenital_macrodactylia|Pancreatic_adenocarcinoma|Transitional_cell_carcinoma_of_the_bladder|Neoplasm_of_stomach|Breast_neoplasm|Brainstem_glioma|Epidermal_nevus|Carcinoma_of_esophagus|Renal_cell_carcinoma,_papillary,_1|Malignant_melanoma_of_skin|Lung_adenocarcinoma|Non-small_cell_lung_cancer|Squamous_cell_lung_carcinoma|Neoplasm_of_brain|Seborrheic_keratosis|Neoplasm_of_ovary|Neoplasm_of_the_large_intestine|Carcinoma_of_colon|Adenocarcinoma_of_stomach|Adenocarcinoma_of_prostate|Lung_carcinoma|Ovarian_Serous_Cystadenocarcinoma|Uterine_Carcinosarcoma|Squamous_cell_carcinoma_of_the_head_and_neck|Megalencephaly-capillary_malformation-polymicrogyria_syndrome|Congenital_lipomatous_overgrowth,_vascular_malformations,_and_epidermal_nevi|Capillary_malformation_of_the_lower_lip,_lymphatic_malformation_of_face_and_neck,_asymmetry_of_face_and_limbs,_and_partial/generalized_overgrowth|Cowden_syndrome_5|Cowden_syndrome|Familial_cancer_of_breast|Glioblastoma|Malignant_tumor_of_floor_of_mouth|Neoplasm_of_uterine_cervix|Malignant_neoplasm_of_body_of_uterus|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0001402,Human_Phenotype_Ontology:HP:0002899,Human_Phenotype_Ontology:HP:0003007,Human_Phenotype_Ontology:HP:0006750,MedGen:C2239176,OMIM:114550,Orphanet:ORPHA88673,SNOMED_CT:187769009,SNOMED_CT:25370001|Human_Phenotype_Ontology:HP:0002885,MONDO:MONDO:0007959,MeSH:D008527,MedGen:C0025149,OMIM:155255,Orphanet:ORPHA616|Human_Phenotype_Ontology:HP:0002889,Human_Phenotype_Ontology:HP:0006744,Human_Phenotype_Ontology:HP:0006759,MeSH:D018268,MedGen:C0206686|Human_Phenotype_Ontology:HP:0004099,MONDO:MONDO:0007962,MedGen:C0265552,OMIM:155500,SNOMED_CT:48449000|Human_Phenotype_Ontology:HP:0006725,MONDO:MONDO:0006047,MedGen:C0281361|Human_Phenotype_Ontology:HP:0006740,MONDO:MONDO:0005611,MedGen:C0279680|Human_Phenotype_Ontology:HP:0006753,MONDO:MONDO:0021085,MeSH:D013274,MedGen:C0038356,SNOMED_CT:126824007|Human_Phenotype_Ontology:HP:0010623,Human_Phenotype_Ontology:HP:0100013,MONDO:MONDO:0021100,MeSH:D001943,MedGen:C1458155,SNOMED_CT:126926005|Human_Phenotype_Ontology:HP:0010796,MONDO:MONDO:0002911,MedGen:C0677865|Human_Phenotype_Ontology:HP:0010816,MONDO:MONDO:0008093,MedGen:C0334082,OMIM:162900,SNOMED_CT:25201003|Human_Phenotype_Ontology:HP:0011459,MONDO:MONDO:0019086,MedGen:C0152018,Orphanet:ORPHA70482|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:0030078,MONDO:MONDO:0005061,MeSH:C538231,MedGen:C0152013|Human_Phenotype_Ontology:HP:0030358,MONDO:MONDO:0005233,MeSH:D002289,MedGen:C0007131,SNOMED_CT:254637007|Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|Human_Phenotype_Ontology:HP:0030692,MONDO:MONDO:0021211,MeSH:D001932,MedGen:C0006118,SNOMED_CT:126952004|Human_Phenotype_Ontology:HP:0031287,MONDO:MONDO:0008420,MedGen:C0022603,OMIM:182000|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:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0005036,MedGen:C0278701|MONDO:MONDO:0005082,MedGen:C0007112|MONDO:MONDO:0005138,MedGen:C0684249|MONDO:MONDO:0006046,MedGen:C0279663|MONDO:MONDO:0006485,MedGen:C0280630|MONDO:MONDO:0010150,MeSH:C535575,MedGen:C1168401,OMIM:275355,Orphanet:ORPHA67037,SNOMED_CT:_716659002|MONDO:MONDO:0011240,MedGen:C1865285,OMIM:602501,Orphanet:ORPHA60040|MONDO:MONDO:0013038,MedGen:C2752042,OMIM:612918,Orphanet:ORPHA140944|MONDO:MONDO:0013125,MedGen:C2751313,OMIM:613089,Orphanet:ORPHA168984|MONDO:MONDO:0014047,MedGen:C3554518,OMIM:615108|MONDO:MONDO:0016063,MedGen:C0018553,OMIM:PS158350,Orphanet:ORPHA201,SNOMED_CT:58037000|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MONDO:MONDO:0018177,MeSH:D005909,MedGen:C0017636,Orphanet:ORPHA360,SNOMED_CT:63634009|MONDO:MONDO:0021320,MedGen:C0153368|MeSH:D002583,MedGen:C0007873,SNOMED_CT:123841004|MedGen:C0153574|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000003.12:g.179234296C>T;GENEINFO=8975:5290;DPVID=12097;DPVSIG=Pathogenic;DPVDSDBID=OMIM:602501;DPVDBN=Megalencephaly-capillary_malformation-polymicrogyria_syndrome;DPVHGVS=NC_000003.12:g.179234296C>T	.