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NM_005029.4(PITX3):c.586G>A (p.Ala196Thr) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 13, 2023
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:
RCV003558976.1

Allele description [Variation Report for NM_005029.4(PITX3):c.586G>A (p.Ala196Thr)]

NM_005029.4(PITX3):c.586G>A (p.Ala196Thr)

Genes:
GBF1:golgi brefeldin A resistant guanine nucleotide exchange factor 1 [Gene - OMIM - HGNC]
PITX3:paired like homeodomain 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q24.32
Genomic location:
Preferred name:
NM_005029.4(PITX3):c.586G>A (p.Ala196Thr)
HGVS:
  • NC_000010.11:g.102230837C>T
  • NG_008147.1:g.15638G>A
  • NG_184036.1:g.285C>T
  • NM_001391923.1:c.-90C>T
  • NM_001391924.1:c.-228C>T
  • NM_005029.4:c.586G>AMANE SELECT
  • NP_005020.1:p.Ala196Thr
  • NC_000010.10:g.103990594C>T
Protein change:
A196T
Molecular consequence:
  • NM_001391923.1:c.-90C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001391924.1:c.-228C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_005029.4:c.586G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004277272Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Dec 13, 2023) 		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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV004277272.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 196 of the PITX3 protein (p.Ala196Thr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PITX3-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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.

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

Last Updated: May 19, 2024