Single allele AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 1, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003448665.1

Allele description [Variation Report for Single allele]

Genes:

DDX52:DExD-box helicase 52 [Gene - OMIM - HGNC]
HNF1B:HNF1 homeobox B [Gene - OMIM - HGNC]
LHX1:LIM homeobox 1 [Gene - OMIM - HGNC]
ACACA:acetyl-CoA carboxylase alpha [Gene - OMIM - HGNC]
AATF:apoptosis antagonizing transcription factor [Gene - OMIM - HGNC]
C17orf78:chromosome 17 open reading frame 78 [Gene - HGNC]
DHRS11:dehydrogenase/reductase 11 [Gene - OMIM - HGNC]
DUSP14:dual specificity phosphatase 14 [Gene - OMIM - HGNC]
GGNBP2:gametogenetin binding protein 2 [Gene - OMIM - HGNC]
MRM1:mitochondrial rRNA methyltransferase 1 [Gene - OMIM - HGNC]
MYO19:myosin XIX [Gene - OMIM - HGNC]
PIGW:phosphatidylinositol glycan anchor biosynthesis class W [Gene - OMIM - HGNC]
SYNRG:synergin gamma [Gene - OMIM - HGNC]
TADA2A:transcriptional adaptor 2A [Gene - OMIM - HGNC]
ZNHIT3:zinc finger HIT-type containing 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q12

Genomic location:

Chr17: 34814816 - 36249107 (on Assembly GRCh37)

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PDR/VanB family oxidoreductase [Mycobacterium avium]
PDR/VanB family oxidoreductase [Mycobacterium avium]
gi|505445478|ref|WP_015632580.1|

Protein
maturase K, partial (chloroplast) [Jacobaea erucifolia]
maturase K, partial (chloroplast) [Jacobaea erucifolia]
gi|21425876|gb|AAM52286.1|

Protein
Jeffreycia usambarensis voucher PE CPG26391 B. Liu et al. 26391 ATP synthase bet...
Jeffreycia usambarensis voucher PE CPG26391 B. Liu et al. 26391 ATP synthase beta subunit (atpB) gene, partial cds; chloroplast
gi|2315907096|gb|ON962019.1|

Nucleotide
tert-Butyl perchlorate (2)
Conserved Domains
Klebsiella variicola strain Kp_HUCA_Bac_59 NODE_135_length_327363_cov_61.153263,...
Klebsiella variicola strain Kp_HUCA_Bac_59 NODE_135_length_327363_cov_61.153263, whole genome shotgun sequence
gi|2154551514|ref|NZ_JAGKYQ01000005 gnl|WGS:NZ_JAGKYQ01|NODE_135_length_327363_cov_61.153263

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004176307	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL CNVClassificationCriteria Aug2020)	Pathogenic (Sep 1, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004176307

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL CNVClassificationCriteria Aug2020)

Pathogenic
(Sep 1, 2023)

unknown

clinical testing

Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV004176307.1

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

Description

This CNV is a 1.4 Mb deletion of 17q12 on chromosome 17 (seq[GRCh37]del(17)(q12),;NC_000017.10:g.34814816_36249107del). The CNV encompasses the following protein coding genes: AATF, ACACA, C17orf78, DDX52, DHRS11, DUSP14, GGNBP2, HNF1B, LHX1, MRM1, MYO19, PIGW, SYNRG, TADA2A, and ZNHIT3. The region of the CNV is flanked by segmental duplications that mediate recurrent breakpoints, and overlaps the well described 17q12 recurrent deletion syndrome (PMID: 27929632). This CNV has not been reported in controls. Based on the available evidence, this CNV is classified as pathogenic.

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

Last Updated: Dec 17, 2023

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