NM_003995.4(NPR2):c.2681A>C (p.Asp894Ala) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 16, 2022
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:: RCV001892856.5

Allele description [Variation Report for NM_003995.4(NPR2):c.2681A>C (p.Asp894Ala)]

NM_003995.4(NPR2):c.2681A>C (p.Asp894Ala)

Gene:

NPR2:natriuretic peptide receptor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9p13.3

Genomic location:

Preferred name:

NM_003995.4(NPR2):c.2681A>C (p.Asp894Ala)

HGVS:

NC_000009.12:g.35807367A>C
NG_009249.1:g.19959A>C
NG_047141.1:g.9906T>G
NM_001378923.1:c.2690A>C
NM_003995.4:c.2681A>CMANE SELECT
NP_001365852.1:p.Asp897Ala
NP_003986.2:p.Asp894Ala
NC_000009.11:g.35807364A>C

Protein change:

D894A

Links:

dbSNP: rs2132095429

NCBI 1000 Genomes Browser:

rs2132095429

Molecular consequence:

NM_001378923.1:c.2690A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003995.4:c.2681A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Acromesomelic dysplasia 1, Maroteaux type (AMD1)
Synonyms:: Acromesomelic dwarfism Maroteux type; ST. HELENA DYSPLASIA; Acromesomelic dysplasia, Maroteaux type; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011275; MedGen: C1864356; Orphanet: 40; OMIM: 602875

Name:: Tall stature-scoliosis-macrodactyly of the great toes syndrome
Synonyms:: Epiphyseal chondrodysplasia, miura type
Identifiers:: MONDO: MONDO:0014401; MedGen: C4014690; Orphanet: 329191; OMIM: 615923

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002154761	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 16, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002154761

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 16, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002154761.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 1383774). This variant has not been reported in the literature in individuals affected with NPR2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with alanine, which is neutral and non-polar, at codon 894 of the NPR2 protein (p.Asp894Ala).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

ClinVar

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