VCV000564286.4 - ClinVar

GRCh37/hg19 16p13.11(chr16:15351247-16458408)x1

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 16p13.11(chr16:15351247-16458408)x1

Variation ID: 564286 Accession: VCV000564286.4

Type and length

copy number loss, 1,107,162 bp

Location

Cytogenetic: 16p13.11 16: 15351247-16458408 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 13, 2022	Feb 13, 2022	Mar 1, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NC_000016.9:g.(?_15351247)_(16458408_?)del

Protein change

Other names

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
MYH11		No evidence available	No evidence available	GRCh38 GRCh38 GRCh37	2035	3806
ABCC1		-	-	GRCh38 GRCh38 GRCh37	140	495
ABCC6		-	-	GRCh38 GRCh38 GRCh37	1470	1833
BMERB1	-	-	-	GRCh38 GRCh38 GRCh37	-	351
CEP20		-	-	GRCh38 GRCh38 GRCh37	19	375
MARF1		-	-	GRCh38 GRCh38 GRCh37	106	455
MPV17L		-	-	GRCh38 GRCh38 GRCh37	-	341
NDE1		-	-	GRCh38 GRCh38 GRCh37	185	1956
NOMO3		-	-	GRCh38 GRCh38 GRCh37	35	307
NPIPA5	-	-	-	GRCh38 GRCh38 GRCh37	2	263

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Pathogenic (1)	no assertion criteria provided	Mar 1, 2021	RCV000683775.4

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Mar 01, 2021)	no assertion criteria provided Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Quest Diagnostics Nichols Institute San Juan Capistrano Accession: SCV000811284.4 First in ClinVar: Sep 30, 2018 Last updated: Feb 13, 2022	Comment: Inherited and de novo deletions involving 16p13.11 have been implicated in variable phenotypes ranging from normalcy to neurodevelopmental disorders with intellectual disability. A male-biased effect … (more) Inherited and de novo deletions involving 16p13.11 have been implicated in variable phenotypes ranging from normalcy to neurodevelopmental disorders with intellectual disability. A male-biased effect has been observed (Tropeano et al. Eur J Hum Genet. 2014 May;22(5). PMID: 24105370; Nagamani et al., Eur J Hum Genet. 2010 19(3):280-6, PMID: 21150890; Hannes et al., 2009. J Med Genet. 46(4):223-32, PMID: 18550696; Ullmann et al., 2007. Hum Mutat. 28(7):674-82, PMID: 17480035). Reduced penetrance and variable expressivity are features of this syndrome. Further, based on a case control study of 16p13.11 copy number variants, there might be a 'sex-limited effect 'on phenotype penetrance as there was a significant enrichment of 16p13.11 deletions amongst male cases, but not amongst female cases (OR=infinity, P=0.001 for males, OR=1.16, P=1.00 for females; Tropeano et al. PLoS One. 2013 Apr 18;8(4):e61365. PMID: 23637818; Tropeano et al., Eur J Hum Genet. 2014 May;22(5). PMID: 24105370). NDE1 (609449) is the strongest candidate gene for the associated neurodevelopmental phenotypes. Other genes likely contribute to the phenotype as well. Biallelic mutation of the NDE1 gene is also associated with the autosomal recessive syndromes of Lissencephaly 4 with microcephaly (OMIM #614019) and microhydranencephaly (#605013). (less)

Comment:

Inherited and de novo deletions involving 16p13.11 have been implicated in variable phenotypes ranging from normalcy to neurodevelopmental disorders with intellectual disability. A male-biased effect has been observed (Tropeano et al. Eur J Hum Genet. 2014 May;22(5). PMID: 24105370; Nagamani et al., Eur J Hum Genet. 2010 19(3):280-6, PMID: 21150890; Hannes et al., 2009. J Med Genet. 46(4):223-32, PMID: 18550696; Ullmann et al., 2007. Hum Mutat. 28(7):674-82, PMID: 17480035). Reduced penetrance and variable expressivity are features of this syndrome. Further, based on a case control study of 16p13.11 copy number variants, there might be a 'sex-limited effect 'on phenotype penetrance as there was a significant enrichment of 16p13.11 deletions amongst male cases, but not amongst female cases (OR=infinity, P=0.001 for males, OR=1.16, P=1.00 for females; Tropeano et al. PLoS One. 2013 Apr 18;8(4):e61365. PMID: 23637818; Tropeano et al., Eur J Hum Genet. 2014 May;22(5). PMID: 24105370). NDE1 (609449) is the strongest candidate gene for the associated neurodevelopmental phenotypes. Other genes likely contribute to the phenotype as well. Biallelic mutation of the NDE1 gene is also associated with the autosomal recessive syndromes of Lissencephaly 4 with microcephaly (OMIM #614019) and microhydranencephaly (#605013).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Mar 26, 2023

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 16p13.11(chr16:15351247-16458408)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...