VCV002944318.1 - ClinVar

NM_003995.4(NPR2):c.2738dup (p.Met913fs)

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

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_003995.4(NPR2):c.2738dup (p.Met913fs)

Variation ID: 2944318 Accession: VCV002944318.1

Type and length

Duplication, 1 bp

Location

Cytogenetic: 9p13.3 9: 35808533-35808534 (GRCh38) [ NCBI UCSC ] 9: 35808530-35808531 (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 29, 2024	Feb 28, 2024	Feb 14, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_003995.4:c.2738dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_003986.2:p.Met913fs	frameshift
NM_001366760.2:c.1201-228dup		intron variant
NM_001378923.1:c.2747dup	NP_001365852.1:p.Met916fs	frameshift
NM_172312.2:c.1373-228dup		intron variant
NC_000009.12:g.35808534dup
NC_000009.11:g.35808531dup
NG_009249.1:g.21126dup
NG_047141.1:g.8739dup

... more HGVS ... less HGVS

Protein change

M913fs, M916fs

Other names

Canonical SPDI

NC_000009.12:35808533:T:TT

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.
NPR2		-	-	GRCh38 GRCh37	442	608
SPAG8		-	-	GRCh38 GRCh37	46	212

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.
Acromesomelic dysplasia 1, Maroteaux type Tall stature-scoliosis-macrodactyly of the great toes syndrome	Pathogenic (1)	criteria provided, single submitter	Feb 14, 2023	RCV003806068.2

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 (Feb 14, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Tall stature-scoliosis-macrodactyly of the great toes syndrome Acromesomelic dysplasia 1, Maroteaux type Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004589430.1 First in ClinVar: Feb 28, 2024 Last updated: Feb 28, 2024	Publications: PubMed (3) PubMed: 15146390‚ 15572448‚ 16384845 Comment: This sequence change creates a premature translational stop signal (p.Met913Ilefs40) in the NPR2 gene. It is expected to result in an absent or disrupted protein … (more) This sequence change creates a premature translational stop signal (p.Met913Ilefs40) in the NPR2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPR2 are known to be pathogenic (PMID: 15146390, 15572448, 16384845). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with NPR2-related conditions. For these reasons, this variant has been classified as Pathogenic. (less)

Comment:

This sequence change creates a premature translational stop signal (p.Met913Ilefs*40) in the NPR2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPR2 are known to be pathogenic (PMID: 15146390, 15572448, 16384845). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with NPR2-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
Heterozygous mutations in natriuretic peptide receptor-B (NPR2) are associated with short stature.	Olney RC	The Journal of clinical endocrinology and metabolism	2006	PMID: 16384845
Critical roles of the guanylyl cyclase B receptor in endochondral ossification and development of female reproductive organs.	Tamura N	Proceedings of the National Academy of Sciences of the United States of America	2004	PMID: 15572448
Mutations in the transmembrane natriuretic peptide receptor NPR-B impair skeletal growth and cause acromesomelic dysplasia, type Maroteaux.	Bartels CF	American journal of human genetics	2004	PMID: 15146390

Text-mined citations for this variant ...

Record last updated Nov 30, 2024

ClinVar Genomic variation as it relates to human health

NM_003995.4(NPR2):c.2738dup (p.Met913fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...