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GRCh38/hg38 16p13.12-13.11(chr16:15032610-16203929) AND 16p13.11 microduplication syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 28, 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:
RCV004555167.1

Allele description [Variation Report for GRCh38/hg38 16p13.12-13.11(chr16:15032610-16203929)]

GRCh38/hg38 16p13.12-13.11(chr16:15032610-16203929)

Genes:
  • ABCC1:ATP binding cassette subfamily C member 1 (ABCC1 blood group) [Gene - OMIM - HGNC]
  • ABCC6:ATP binding cassette subfamily C member 6 [Gene - OMIM - HGNC]
  • LOC121587532:BRD4-independent group 4 enhancer GRCh37_chr16:15972689-15973888 [Gene]
  • LOC126862299:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:15693082-15694281 [Gene]
  • LOC129390770:MPRA-validated peak2507 silencer [Gene]
  • MPV17L:MPV17 mitochondrial inner membrane protein like [Gene - OMIM - HGNC]
  • MPV17L-BMERB1:MPV17L-BMERB1 readthrough [Gene]
  • NTAN1:N-terminal asparagine amidase [Gene - OMIM - HGNC]
  • NOMO1:NODAL modulator 1 [Gene - OMIM - HGNC]
  • NOMO3:NODAL modulator 3 [Gene - OMIM - HGNC]
  • LOC126862298:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:15587399-15588598 [Gene]
  • LOC121847972:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:15684383-15685582 [Gene]
  • LOC126862300:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:15993095-15994294 [Gene]
  • LOC131696449:PKD1P1-NPIPA5L readthrough [Gene]
  • RRN3:RRN3 homolog, RNA polymerase I transcription factor [Gene - OMIM - HGNC]
  • LOC121847973:Sharpr-MPRA regulatory region 10508 [Gene]
  • LOC112340383:Sharpr-MPRA regulatory region 11301 [Gene]
  • LOC112340381:Sharpr-MPRA regulatory region 12074 [Gene]
  • LOC112340379:Sharpr-MPRA regulatory region 1380 [Gene]
  • LOC112340378:Sharpr-MPRA regulatory region 13846 [Gene]
  • LOC125146421:Sharpr-MPRA regulatory region 15590 [Gene]
  • LOC112340377:Sharpr-MPRA regulatory region 1947 [Gene]
  • LOC125146418:Sharpr-MPRA regulatory region 4661 [Gene]
  • LOC112340382:Sharpr-MPRA regulatory region 4662 [Gene]
  • LOC113939949:Sharpr-MPRA regulatory region 5546 [Gene]
  • LOC125146419:Sharpr-MPRA regulatory region 7034 [Gene]
  • LOC125146420:Sharpr-MPRA regulatory region 7660 [Gene]
  • LOC112340380:Sharpr-MPRA regulatory region 9672 [Gene]
  • BMERB1:bMERB domain containing 1 [Gene - HGNC]
  • CEP20:centrosomal protein 20 [Gene - OMIM - HGNC]
  • MARF1:meiosis regulator and mRNA stability factor 1 [Gene - OMIM - HGNC]
  • MIR1972-1:microRNA 1972-1 [Gene - HGNC]
  • MIR3179-1:microRNA 3179-1 [Gene - HGNC]
  • MIR3179-2:microRNA 3179-2 [Gene - HGNC]
  • MIR3180-1:microRNA 3180-1 [Gene - HGNC]
  • MIR3180-2:microRNA 3180-2 [Gene - HGNC]
  • MIR3180-4:microRNA 3180-4 [Gene - HGNC]
  • MIR3670-1:microRNA 3670-1 [Gene - HGNC]
  • MIR3670-2:microRNA 3670-2 [Gene - HGNC]
  • MIR484:microRNA 484 [Gene - HGNC]
  • MIR6506:microRNA 6506 [Gene - HGNC]
  • MIR6511A1:microRNA 6511a-1 [Gene - HGNC]
  • MIR6511A2:microRNA 6511a-2 [Gene - HGNC]
  • MIR6511A3:microRNA 6511a-3 [Gene - HGNC]
  • MIR6511B2:microRNA 6511b-2 [Gene - HGNC]
  • MIR6770-1:microRNA 6770-1 [Gene - HGNC]
  • MIR6770-2:microRNA 6770-2 [Gene - HGNC]
  • MYH11:myosin heavy chain 11 [Gene - OMIM - HGNC]
  • NPIPA1:nuclear pore complex interacting protein family member A1 [Gene - OMIM - HGNC]
  • NPIPA2:nuclear pore complex interacting protein family member A2 [Gene - HGNC]
  • NPIPA3:nuclear pore complex interacting protein family member A3 [Gene - HGNC]
  • NPIPA5:nuclear pore complex interacting protein family member A5 [Gene - HGNC]
  • NPIPA7:nuclear pore complex interacting protein family member A7 [Gene - HGNC]
  • NPIPA6:nuclear pore complex interacting protein family, member A6 [Gene - HGNC]
  • NDE1:nudE neurodevelopment protein 1 [Gene - OMIM - HGNC]
  • PLA2G10:phospholipase A2 group X [Gene - OMIM - HGNC]
  • PDXDC1:pyridoxal dependent decarboxylase domain containing 1 [Gene - OMIM - HGNC]
  • LOC100288162:uncharacterized LOC100288162 [Gene]
  • LOC100505915:uncharacterized LOC100505915 [Gene]
Variant type:
copy number gain
Cytogenetic location:
16p13.12-13.11
Genomic location:
Chr16: 14679387 - 16530762 (on Assembly GRCh38)
Preferred name:
GRCh38/hg38 16p13.12-13.11(chr16:15032610-16203929)
Observations:
1

Condition(s)

Name:
16p13.11 microduplication syndrome
Identifiers:
MONDO: MONDO:0016837; MedGen: C4304595

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005044087New York Genome Center - PrenatalSEQ
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Likely pathogenic
(Apr 28, 2023) 		inheritedclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedunknown1not providednot provided1not providedclinical testing

Citations

PubMed

Refining the Phenotype of Recurrent Rearrangements of Chromosome 16.

Redaelli S, Maitz S, Crosti F, Sala E, Villa N, Spaccini L, Selicorni A, Rigoldi M, Conconi D, Dalprà L, Roversi G, Bentivegna A.

Int J Mol Sci. 2019 Mar 4;20(5). doi:pii: E1095. 10.3390/ijms20051095.

PubMed [citation]
PMID:
30836598
PMCID:
PMC6429492

The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left heart disease.

Warburton D, Ronemus M, Kline J, Jobanputra V, Williams I, Anyane-Yeboa K, Chung W, Yu L, Wong N, Awad D, Yu CY, Leotta A, Kendall J, Yamrom B, Lee YH, Wigler M, Levy D.

Hum Genet. 2014 Jan;133(1):11-27. doi: 10.1007/s00439-013-1353-9. Epub 2013 Aug 25.

PubMed [citation]
PMID:
23979609
PMCID:
PMC3880624
See all PubMed Citations (4)

Details of each submission

From New York Genome Center - PrenatalSEQ, SCV005044087.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (4)

Description

The inherited 16p13.11 copy number gain identified on the short arm of chromosome 16 is associated with a recurrent microduplication syndrome. This duplication is curated by ClinGen Dosage Sensitivity Working Group and given a Triplosensitivity Score of 2 [https://search.clinicalgenome.org/kb/gene-dosage/region/ISCA-37415]. Segmental duplications within this region make mapping of the exact breakpoints with whole genome sequencing difficult, however, microarray analysis confirms a minimal duplication region containing NTAN1 at the telomeric breakpoint and ABCC6 at the centromeric breakpoint. This duplication does contain genes MARF1, NDE1, MYH11 and FOPNL, which are often considered the smallest region of overlap for recurrent variation in the 16p13 region. Similar duplications have been observed in affected individuals in the literature with variable clinical phenotypes including neurodevelopmental phenotypes, variable dysmorphic features, hypotonia, congenital heart defects and additional congenital malformations [PMID:30836598, 23979609, 30287593, 21150890]. Alvarado et al found an enrichment of chromosome 16p13.1 duplication in a cohort of patients affected with isolated talipes equinovarus though the clinical significance of this association is uncertain at this time [PMID:22892537]. While some 16p13.11 duplications are identified de novo in affected individuals, many are found to be inherited from asymptomatic or mildly affected parents [PMID:30836598, 21614007, 30287593], and 16p13.11 duplications are also identified in control populations [PMID:23637818, 21844811, 24352232] supporting the observation of reduced penetrance and variable expressivity for 16p13.11 duplications. The inherited 16p13.11 duplication is classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: Sep 1, 2024