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NM_003924.4(PHOX2B):c.520A>G (p.Lys174Glu) AND Haddad syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 18, 2019
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:
RCV001206389.8

Allele description [Variation Report for NM_003924.4(PHOX2B):c.520A>G (p.Lys174Glu)]

NM_003924.4(PHOX2B):c.520A>G (p.Lys174Glu)

Gene:
PHOX2B:paired like homeobox 2B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4p13
Genomic location:
Preferred name:
NM_003924.4(PHOX2B):c.520A>G (p.Lys174Glu)
HGVS:
  • NC_000004.12:g.41746232T>C
  • NG_008243.1:g.7739A>G
  • NM_003924.4:c.520A>GMANE SELECT
  • NP_003915.2:p.Lys174Glu
  • LRG_513t1:c.520A>G
  • LRG_513:g.7739A>G
  • NC_000004.11:g.41748249T>C
  • NM_003924.3:c.520A>G
Protein change:
K174E
Links:
dbSNP: rs1733895906
NCBI 1000 Genomes Browser:
rs1733895906
Molecular consequence:
  • NM_003924.4:c.520A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Haddad syndrome (OHD)
Synonyms:
Ondine-Hirschsprung disease
Identifiers:
MONDO: MONDO:0020493; MedGen: C1859049; Orphanet: 99803

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001377696Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 18, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001377696.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C55"). This variant has not been reported in the literature in individuals with PHOX2B-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces lysine with glutamic acid at codon 174 of the PHOX2B protein (p.Lys174Glu). The lysine residue is highly conserved and there is a small physicochemical difference between lysine and glutamic acid.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024