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Single allele AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 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:
RCV003448696.1

Allele description [Variation Report for Single allele]

Genes:
  • CD274:CD274 molecule [Gene - OMIM - HGNC]
  • DOCK8-AS1:DOCK8 antisense RNA 1 [Gene - HGNC]
  • FREM1:FRAS1 related extracellular matrix 1 [Gene - OMIM - HGNC]
  • GLIS3:GLIS family zinc finger 3 [Gene - OMIM - HGNC]
  • JAK2:Janus kinase 2 [Gene - OMIM - HGNC]
  • KANK1:KN motif and ankyrin repeat domains 1 [Gene - OMIM - HGNC]
  • PSIP1:PC4 and SRSF1 interacting protein 1 [Gene - OMIM - HGNC]
  • RANBP6:RAN binding protein 6 [Gene - HGNC]
  • RIC1:RIC1 homolog, RAB6A GEF complex partner 1 [Gene - OMIM - HGNC]
  • RCL1:RNA terminal phosphate cyclase like 1 [Gene - OMIM - HGNC]
  • SMARCA2:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 [Gene - OMIM - HGNC]
  • TPD52L3:TPD52 like 3 [Gene - OMIM - HGNC]
  • AK3:adenylate kinase 3 [Gene - OMIM - HGNC]
  • BNC2:basonuclin zinc finger protein 2 [Gene - OMIM - HGNC]
  • BRD10:bromodomain containing 10 [Gene - HGNC]
  • CDC37L1:cell division cycle 37 like 1, HSP90 cochaperone [Gene - OMIM - HGNC]
  • CER1:cerberus 1, DAN family BMP antagonist [Gene - OMIM - HGNC]
  • CCDC171:coiled-coil domain containing 171 [Gene - HGNC]
  • DOCK8:dedicator of cytokinesis 8 [Gene - OMIM - HGNC]
  • DMAC1:distal membrane arm assembly component 1 [Gene - OMIM - HGNC]
  • DMRT1:doublesex and mab-3 related transcription factor 1 [Gene - OMIM - HGNC]
  • DMRT2:doublesex and mab-3 related transcription factor 2 [Gene - OMIM - HGNC]
  • DMRT3:doublesex and mab-3 related transcription factor 3 [Gene - OMIM - HGNC]
  • ERMP1:endoplasmic reticulum metallopeptidase 1 [Gene - OMIM - HGNC]
  • GLDC:glycine decarboxylase [Gene - OMIM - HGNC]
  • INSL4:insulin like 4 [Gene - OMIM - HGNC]
  • INSL6:insulin like 6 [Gene - OMIM - HGNC]
  • IL33:interleukin 33 [Gene - OMIM - HGNC]
  • LURAP1L:leucine rich adaptor protein 1 like [Gene - OMIM - HGNC]
  • KDM4C:lysine demethylase 4C [Gene - OMIM - HGNC]
  • MLANA:melan-A [Gene - OMIM - HGNC]
  • MIR101-2:microRNA 101-2 [Gene - OMIM - HGNC]
  • MPDZ:multiple PDZ domain crumbs cell polarity complex component [Gene - OMIM - HGNC]
  • NFIB:nuclear factor I B [Gene - OMIM - HGNC]
  • PLPP6:phospholipid phosphatase 6 [Gene - OMIM - HGNC]
  • PLGRKT:plasminogen receptor with a C-terminal lysine [Gene - OMIM - HGNC]
  • KCNV2:potassium voltage-gated channel modifier subfamily V member 2 [Gene - OMIM - HGNC]
  • PDCD1LG2:programmed cell death 1 ligand 2 [Gene - OMIM - HGNC]
  • PTPRD:protein tyrosine phosphatase receptor type D [Gene - OMIM - HGNC]
  • PUM3:pumilio RNA binding family member 3 [Gene - OMIM - HGNC]
  • RFX3:regulatory factor X3 [Gene - OMIM - HGNC]
  • RLN1:relaxin 1 [Gene - OMIM - HGNC]
  • RLN2:relaxin 2 [Gene - OMIM - HGNC]
  • SNAPC3:small nuclear RNA activating complex polypeptide 3 [Gene - OMIM - HGNC]
  • SLC1A1:solute carrier family 1 member 1 [Gene - OMIM - HGNC]
  • SPATA6L:spermatogenesis associated 6 like [Gene - HGNC]
  • TTC39B:tetratricopeptide repeat domain 39B [Gene - OMIM - HGNC]
  • TYRP1:tyrosinase related protein 1 [Gene - OMIM - HGNC]
  • UHRF2:ubiquitin like with PHD and ring finger domains 2 [Gene - OMIM - HGNC]
  • VLDLR:very low density lipoprotein receptor [Gene - OMIM - HGNC]
  • ZDHHC21:zinc finger DHHC-type palmitoyltransferase 21 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9p24.3-22.3
Genomic location:
Chr9: 204064 - 16456192 (on Assembly GRCh37)

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004176338Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL CNVClassificationCriteria Aug2020)		Pathogenic
(Jun 1, 2023) 		unknownclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV004176338.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This CNV is a 16.3 Mb deletion of 9p24.3-p22.3 on chromosome 9, seq[GRCh37]del(9)(p24.3p22.3), NC_000009.11:g.204064_16456192del. The CNV encompasses 49 protein coding genes including the NFIB gene and overlaps the proposed critical regions of the well described 9p deletion syndrome (PMID: 35047865). The NFIB gene encodes nuclear factor 1 B, a transcription factor that regulates mammalian development. Haploinsufficiency of NFIB is associated with acquired macrocephaly with impaired intellectual development (MIM 600728). The CNV has not been reported in published controls and is not present in the Database of Genomic Variants (PMID: 24174537). Based on the available evidence, this CNV is classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 1, 2024