Single allele AND Renal transitional cell carcinoma

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 14, 2019
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000754611.2

Allele description [Variation Report for Single allele]

Genes:

AGBL3:AGBL carboxypeptidase 3 [Gene - OMIM - HGNC]
ATP6V0A4:ATPase H+ transporting V0 subunit a4 [Gene - OMIM - HGNC]
BRAF:B-Raf proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
CLEC2L:C-type lectin domain family 2 member L [Gene - HGNC]
CNOT4:CCR4-NOT transcription complex subunit 4 [Gene - OMIM - HGNC]
COPG2:COPI coat complex subunit gamma 2 [Gene - OMIM - HGNC]
DENND2A:DENN domain containing 2A [Gene - OMIM - HGNC]
FMC1-LUC7L2:FMC1-LUC7L2 readthrough [Gene - HGNC]
KIAA1549:KIAA1549 [Gene - OMIM - HGNC]
KLF14:KLF transcription factor 14 [Gene - OMIM - HGNC]
LUC7L2:LUC7 like 2, pre-mRNA splicing factor [Gene - OMIM - HGNC]
MESTIT1:MEST intronic transcript 1, antisense RNA [Gene - OMIM - HGNC]
NDUFB2:NADH:ubiquinone oxidoreductase subunit B2 [Gene - OMIM - HGNC]
RAB19:RAB19, member RAS oncogene family [Gene - HGNC]
SVOPL:SVOP like [Gene - OMIM - HGNC]
WDR91:WD repeat domain 91 [Gene - OMIM - HGNC]
ADCK2:aarF domain containing kinase 2 [Gene - HGNC]
AKR1B10:aldo-keto reductase family 1 member B10 [Gene - OMIM - HGNC]
AKR1B15:aldo-keto reductase family 1 member B15 [Gene - OMIM - HGNC]
AKR1B1:aldo-keto reductase family 1 member B [Gene - OMIM - HGNC]
AKR1D1:aldo-keto reductase family 1 member D1 [Gene - OMIM - HGNC]
BPGM:bisphosphoglycerate mutase [Gene - OMIM - HGNC]
CREB3L2:cAMP responsive element binding protein 3 like 2 [Gene - OMIM - HGNC]
CALD1:caldesmon 1 [Gene - OMIM - HGNC]
CPA1:carboxypeptidase A1 [Gene - OMIM - HGNC]
CPA2:carboxypeptidase A2 [Gene - OMIM - HGNC]
CPA4:carboxypeptidase A4 [Gene - OMIM - HGNC]
CPA5:carboxypeptidase A5 [Gene - OMIM - HGNC]
CYREN:cell cycle regulator of NHEJ [Gene - OMIM - HGNC]
CEP41:centrosomal protein 41 [Gene - OMIM - HGNC]
CHRM2:cholinergic receptor muscarinic 2 [Gene - OMIM - HGNC]
CHCHD3:coiled-coil-helix-coiled-coil-helix domain containing 3 [Gene - OMIM - HGNC]
DGKI:diacylglycerol kinase iota [Gene - OMIM - HGNC]
EXOC4:exocyst complex component 4 [Gene - OMIM - HGNC]
FAM180A:family with sequence similarity 180 member A [Gene - HGNC]
FMC1:formation of mitochondrial complex V assembly factor 1 homolog [Gene - OMIM - HGNC]
IFT56:intraflagellar transport 56 [Gene - OMIM - HGNC]
KLHDC10:kelch domain containing 10 [Gene - OMIM - HGNC]
KLRG2:killer cell lectin like receptor G2 [Gene - HGNC]
LRGUK:leucine rich repeats and guanylate kinase domain containing [Gene - OMIM - HGNC]
LUZP6:leucine zipper protein 6 [Gene - OMIM - HGNC]
KDM7A:lysine demethylase 7A [Gene - OMIM - HGNC]
MKRN1:makorin ring finger protein 1 [Gene - OMIM - HGNC]
MEST:mesoderm specific transcript [Gene - OMIM - HGNC]
MIR182:microRNA 182 [Gene - OMIM - HGNC]
MIR183:microRNA 183 [Gene - OMIM - HGNC]
MIR29A:microRNA 29a [Gene - OMIM - HGNC]
MIR29B1:microRNA 29b-1 [Gene - OMIM - HGNC]
MIR335:microRNA 335 [Gene - OMIM - HGNC]
MIR96:microRNA 96 [Gene - OMIM - HGNC]
MKLN1:muskelin 1 [Gene - OMIM - HGNC]
MTPN:myotrophin [Gene - OMIM - HGNC]
NRF1:nuclear respiratory factor 1 [Gene - OMIM - HGNC]
NUP205:nucleoporin 205 [Gene - OMIM - HGNC]
PTN:pleiotrophin [Gene - OMIM - HGNC]
PLXNA4:plexin A4 [Gene - OMIM - HGNC]
PODXL:podocalyxin like [Gene - OMIM - HGNC]
PARP12:poly(ADP-ribose) polymerase family member 12 [Gene - OMIM - HGNC]
SSMEM1:serine rich single-pass membrane protein 1 [Gene - HGNC]
STMP1:short transmembrane mitochondrial protein 1 [Gene - OMIM - HGNC]
SLC13A4:solute carrier family 13 member 4 [Gene - OMIM - HGNC]
SLC35B4:solute carrier family 35 member B4 [Gene - OMIM - HGNC]
SLC37A3:solute carrier family 37 member 3 [Gene - OMIM - HGNC]
STRA8:stimulated by retinoic acid 8 [Gene - OMIM - HGNC]
TSGA13:testis specific 13 [Gene - HGNC]
TBXAS1:thromboxane A synthase 1 [Gene - OMIM - HGNC]
TMEM140:transmembrane protein 140 [Gene - HGNC]
TMEM209:transmembrane protein 209 [Gene - HGNC]
TMEM213:transmembrane protein 213 [Gene - HGNC]
TRIM24:tripartite motif containing 24 [Gene - OMIM - HGNC]
UBN2:ubinuclein 2 [Gene - OMIM - HGNC]
UBE2H:ubiquitin conjugating enzyme E2 H [Gene - OMIM - HGNC]
LOC101928861:uncharacterized LOC101928861 [Gene]
ZC3HC1:zinc finger C3HC-type containing 1 [Gene - OMIM - HGNC]
ZC3HAV1L:zinc finger CCCH-type containing, antiviral 1 like [Gene - HGNC]
ZC3HAV1:zinc finger CCCH-type containing, antiviral 1 [Gene - OMIM - HGNC]

Variant type:

Complex

Cytogenetic location:

7q32.2-34

Genomic location:

Chr7: 129367205 - 140482957 (on Assembly GRCh37)

HGVS:

Functional consequence:

variation affecting protein structure [Variation Ontology: 0060]

Observations:

Condition(s)

Name:: Renal transitional cell carcinoma
Identifiers:: MedGen: C1319314; Human Phenotype Ontology: HP:0030409

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Homo sapiens chromosome 3 putative open reading frame 36 (C3orf36), long non-cod...
Homo sapiens chromosome 3 putative open reading frame 36 (C3orf36), long non-coding RNA
gi|1607263963|ref|NR_161373.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000864217	Molecular Pathology Diagnostics Labratory, University of Iowa Hospitals & Clinics	no assertion criteria provided	Likely pathogenic (Jan 14, 2019)	somatic	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000864217

Molecular Pathology Diagnostics Labratory, University of Iowa Hospitals & Clinics

no assertion criteria provided

Likely pathogenic
(Jan 14, 2019)

somatic

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
Caucasian	somatic	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Molecular Pathology Diagnostics Labratory, University of Iowa Hospitals & Clinics, SCV000864217.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Caucasian	1	not provided	not provided	clinical testing	not provided

Description

This particular fusion has not been functionally characterized, however, Ross, 2016 analyzed 20,573 cases of solid tumors and detected BRAF fusions that contained the entire kinase domain in fifty-five cases. BRAF fusions were shown to be activating and oncogenic (Ross, 2016; Botton, 2013; Ciampi, 2005; Jones, 2008; Palanisamy, 2010).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	somatic	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Jun 23, 2024

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