VCV000218968.4 - ClinVar

t(5;16)(p15.31;q23.1)

Germline

Classification

no assertion criteria provided. Learn more about how ClinVar calculates review status.

Likely pathogenic

This classification is based on the single submission received

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.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

t(5;16)(p15.31;q23.1)

Variation ID: 218968 Accession: VCV000218968.4

Type and length

Translocation, -

Location

Cytogenetic: 5p15.33-15.31 16q23.1-24.3 16: 76935310-90354753 (GRCh37) [ NCBI UCSC ] 5: 1-8180513 (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	Jan 13, 2016	Apr 13, 2025	Nov 24, 2015

HGVS

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.
ANKRD11		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	2907	3082
FOXC2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	169	287
FOXF1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	202	258
TERT		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	3186	3648
ACSF3		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	923	1131
ADAMTS18		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	1163	1283
CA5A		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	211	281
CDT1		Gene associated with autosomal recessive phenotype	Not yet evaluated	GRCh38 GRCh37	455	571
CHMP1A		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	216	296
DNAAF1		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	647	744

There are 142 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh37 , GRCh37) and ClinGen Dosage Sensitivity Map.

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	Likely pathogenic (1)	no assertion criteria provided	Nov 24, 2015	RCV000203391.4

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.
Likely pathogenic (Nov 24, 2015) C Contributing to aggregate classification	no assertion criteria provided Method: research	not provided (Other) Affected status: yes Allele origin: unknown	Advanced Center For Translational And Genetic Medicine, Ann & Robert H. Lurie Children's Hospital Of Chicago Accession: SCV000257401.3 First in ClinVar: Jan 13, 2016 Last updated: Apr 13, 2025	Publications: PubMed (1) PubMed: 20503335 Observation 1: Number of individuals with the variant: 1 Clinical Features: Neonatal hypotonia (present) , External genital hypoplasia (present) , Short stature (present) , Motor delay (present) , Intellectual disability (present) , Prominent forehead (present) , Wide nasal bridge (present) , Low-set ears (present) , High palate (present) , Abnormality of upper lip (present) , Delayed speech and language development (present) , Stridor (present) , Dolichocephaly (present) , Stereotypic behavior (present) , Cat cry (present) , Clubbing (present) , Swelling of proximal interphalangeal joints (present) , Distal lower limb amyotrophy (present) , Narrow chest (present) , Pes planus (present) Indication for testing: Intellectual disability Family history: yes Age: 10-19 years Sex: male Geographic origin: Turkey Tissue: Blood Observation 2: Number of individuals with the variant: 1 Clinical Features: Neonatal hypotonia (present) , External genital hypoplasia (present) , Short stature (present) , Motor delay (present) , Intellectual disability (present) , Prominent forehead (present) , Wide nasal bridge (present) , Low-set ears (present) , High palate (present) , Abnormality of upper lip (present) , Delayed speech and language development (present) , Stridor (present) , Dolichocephaly (present) , Stereotypic behavior (present) , Clubbing (present) , Swelling of proximal interphalangeal joints (present) , Distal lower limb amyotrophy (present) , Narrow chest (present) , Pes planus (present) Indication for testing: Intellectual disability Family history: yes Age: 0-9 years Sex: male Geographic origin: Turkey Tissue: Blood

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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
A t(5;16) translocation is the likely driver of a syndrome with ambiguous genitalia, facial dysmorphism, intellectual disability, and speech delay.	Ozantürk A	Cold Spring Harbor molecular case studies	2016	PMID: 27148584
A t(5;16)(p15.32;q23.3) generating 16q23.3 --> qter duplication and 5p15.32 --> pter deletion in two siblings with mental retardation, dysmorphic features, and speech delay.	Hellani A	American journal of medical genetics. Part A	2010	PMID: 20503335

Text-mined citations for this variant ...

Record last updated Apr 13, 2025

ClinVar Genomic variation as it relates to human health

t(5;16)(p15.31;q23.1)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...