VCV002424617.27 - ClinVar

NC_000005.9:g.(?_176289625)_(177151363_?)del

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.

(2)

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

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000005.9:g.(?_176289625)_(177151363_?)del

Variation ID: 2424617 Accession: VCV002424617.27

Type and length

Deletion, 861,739 bp

Location

Cytogenetic: 5q35.2-35.3 5: 176289625-177151363 (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, 2023	Nov 11, 2023	Oct 21, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NC_000005.9:g.(?_176289625)_(177151363_?)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.
DDX41		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	573	641
NSD1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1740	1856
B4GALT7		-	-	GRCh38 GRCh37	326	417
DBN1		-	-	GRCh38 GRCh37	50	114
DOK3		-	-	GRCh38 GRCh37	52	126
F12		-	-	GRCh38 GRCh37	158	239
FAM153A	-	-	-	GRCh38 GRCh37	19	74
FAM193B		-	-	GRCh38 GRCh37	62	127
FGFR4		-	-	GRCh38 GRCh37	70	132
GRK6		-	-	GRCh38 GRCh37	13	86

There are 14 more genes affected by this variant. See the full set of genes in Variation Viewer (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	no classifications from unflagged records (1)	no classifications from unflagged records	-	RCV003113198.13
Sotos syndrome	Pathogenic (1)	criteria provided, single submitter	Oct 21, 2022	RCV003232856.9

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 (Oct 21, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	None Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003791916.2 First in ClinVar: Feb 13, 2023 Last updated: Jun 10, 2023	Publications: PubMed (7) PubMed: 12464997‚ 14571271‚ 15942875‚ 16247291‚ 18505455‚ 21597970‚ 25608832 Comment: A gross deletion of the genomic region encompassing the full coding sequence of the NSD1 gene has been identified. Loss-of-function variants in NSD1 are known … (more) A gross deletion of the genomic region encompassing the full coding sequence of the NSD1 gene has been identified. Loss-of-function variants in NSD1 are known to be pathogenic (PMID: 12464997, 14571271, 15942875, 16247291). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. A similar copy number variant has been observed in individuals with Sotos syndrome (PMID: 18505455, 21597970, 25608832). For these reasons, this variant has been classified as Pathogenic. (less)
Pathogenic (Oct 21, 2022)	Flagged submission flagged submission (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003791281 appears to (...more) Source: NCBI	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003791281.2 First in ClinVar: Feb 13, 2023 Last updated: Nov 11, 2023	Publications: PubMed (1) PubMed: 26047794 Comment: A gross deletion of the genomic region encompassing the full coding sequence of the SLC34A1 gene has been identified. Loss-of-function variants in SLC34A1 are known … (more) A gross deletion of the genomic region encompassing the full coding sequence of the SLC34A1 gene has been identified. Loss-of-function variants in SLC34A1 are known to be pathogenic (PMID: 26047794). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with SLC34A1-related conditions. For these reasons, this variant has been classified as Pathogenic. (less)
Flagged submissions do not contribute to the aggregate classification or review status for the variant. Learn more

Comment:

A gross deletion of the genomic region encompassing the full coding sequence of the NSD1 gene has been identified. Loss-of-function variants in NSD1 are known to be pathogenic (PMID: 12464997, 14571271, 15942875, 16247291). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. A similar copy number variant has been observed in individuals with Sotos syndrome (PMID: 18505455, 21597970, 25608832). For these reasons, this variant has been classified as Pathogenic.

Comment:

A gross deletion of the genomic region encompassing the full coding sequence of the SLC34A1 gene has been identified. Loss-of-function variants in SLC34A1 are known to be pathogenic (PMID: 26047794). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with SLC34A1-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Title	Author	Journal	Year	Link
Autosomal-Recessive Mutations in SLC34A1 Encoding Sodium-Phosphate Cotransporter 2A Cause Idiopathic Infantile Hypercalcemia.	Schlingmann KP	Journal of the American Society of Nephrology : JASN	2016	PMID: 26047794
Detecting copy-number variations in whole-exome sequencing data using the eXome Hidden Markov Model: an 'exome-first' approach.	Miyatake S	Journal of human genetics	2015	PMID: 25608832
Sotos syndrome, infantile hypercalcemia, and nephrocalcinosis: a contiguous gene syndrome.	Kenny J	Pediatric nephrology (Berlin, Germany)	2011	PMID: 21597970
Alu-related 5q35 microdeletions in Sotos syndrome.	Mochizuki J	Clinical genetics	2008	PMID: 18505455
NSD1 analysis for Sotos syndrome: insights and perspectives from the clinical laboratory.	Waggoner DJ	Genetics in medicine : official journal of the American College of Medical Genetics	2005	PMID: 16247291
Genotype-phenotype associations in Sotos syndrome: an analysis of 266 individuals with NSD1 aberrations.	Tatton-Brown K	American journal of human genetics	2005	PMID: 15942875
Mutations in NSD1 are responsible for Sotos syndrome, but are not a frequent finding in other overgrowth phenotypes.	Türkmen S	European journal of human genetics : EJHG	2003	PMID: 14571271
NSD1 mutations are the major cause of Sotos syndrome and occur in some cases of Weaver syndrome but are rare in other overgrowth phenotypes.	Douglas J	American journal of human genetics	2003	PMID: 12464997

Text-mined citations for this variant ...

Record last updated Nov 03, 2024

ClinVar Genomic variation as it relates to human health

NC_000005.9:g.(?_176289625)_(177151363_?)del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...