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NM_002204.4(ITGA3):c.864_867del (p.Gly289fs) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 8, 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:
RCV001009285.1

Allele description [Variation Report for NM_002204.4(ITGA3):c.864_867del (p.Gly289fs)]

NM_002204.4(ITGA3):c.864_867del (p.Gly289fs)

Gene:
ITGA3:integrin subunit alpha 3 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
17q21.33
Genomic location:
Preferred name:
NM_002204.4(ITGA3):c.864_867del (p.Gly289fs)
HGVS:
  • NC_000017.11:g.50071419AGGC[1]
  • NC_000017.11:g.50071419_50071422AGGC[1]
  • NG_029107.2:g.20444AGGC[1]
  • NM_002204.4:c.864_867delMANE SELECT
  • NP_002195.1:p.Gly289fs
  • NC_000017.10:g.48148783AGGC[1]
  • NM_002204.2:c.864_867delAGGC
Protein change:
G289fs
Links:
dbSNP: rs1598186840
NCBI 1000 Genomes Browser:
rs1598186840
Molecular consequence:
  • NM_002204.4:c.864_867del - 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
SCV001169107GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Mar 8, 2019) 		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, SCV001169107.1

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

Description

The c.864_867delAGGC variant in the ITGA3 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.864_867delAGGC variant causes a frameshift starting with codon Glycine 289, changes this amino acid to a Glutamic Acid residue, and creates a premature Stop codon at position 27 of the new reading frame, denoted p.Gly289GlufsX27. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.864_867delAGGC variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.864_867delAGGC as a likely pathogenic variant.

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

Last Updated: Apr 23, 2022