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NM_001372076.1(PAX9):c.114_117dup (p.Cys40fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 14, 2017
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:
RCV000478656.2

Allele description [Variation Report for NM_001372076.1(PAX9):c.114_117dup (p.Cys40fs)]

NM_001372076.1(PAX9):c.114_117dup (p.Cys40fs)

Gene:
PAX9:paired box 9 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
14q13.3
Genomic location:
Preferred name:
NM_001372076.1(PAX9):c.114_117dup (p.Cys40fs)
HGVS:
  • NC_000014.9:g.36663006_36663009dup
  • NG_013357.1:g.10439_10442dup
  • NM_001372076.1:c.114_117dupMANE SELECT
  • NM_006194.4:c.114_117dup
  • NP_001359005.1:p.Cys40fs
  • NP_006185.1:p.Cys40fs
  • NC_000014.8:g.37132211_37132214dup
  • NM_006194.3:c.114_117dupACCG
Protein change:
C40fs
Links:
dbSNP: rs1555316699
NCBI 1000 Genomes Browser:
rs1555316699
Molecular consequence:
  • NM_001372076.1:c.114_117dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_006194.4:c.114_117dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000566380GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Sep 14, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000566380.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.114_117dupACCG variant in the PAX9 gene has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.114_117dupACCG variant causes a frameshift starting with codon Cysteine 40, changes this amino acid to a Threonine residue, and creates a premature Stop codon at position 3 of the new reading frame, denoted p.Cys40ThrfsX3. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.114_117dupACCG variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.114_117dupACCG as a pathogenic variant.

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

Last Updated: Apr 23, 2022