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NM_001903.5(CTNNA1):c.1246_1249del (p.Val416fs) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 20, 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:
RCV001054842.4

Allele description [Variation Report for NM_001903.5(CTNNA1):c.1246_1249del (p.Val416fs)]

NM_001903.5(CTNNA1):c.1246_1249del (p.Val416fs)

Gene:
CTNNA1:catenin alpha 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
5q31.2
Genomic location:
Preferred name:
NM_001903.5(CTNNA1):c.1246_1249del (p.Val416fs)
HGVS:
  • NC_000005.10:g.138887592_138887595del
  • NG_047029.1:g.139197_139200del
  • NM_001290307.3:c.1246_1249del
  • NM_001290309.3:c.937_940del
  • NM_001290310.3:c.877_880del
  • NM_001290312.1:c.136_139del
  • NM_001323982.2:c.1246_1249del
  • NM_001323983.1:c.1246_1249del
  • NM_001323984.2:c.1246_1249del
  • NM_001323985.2:c.1246_1249del
  • NM_001323986.2:c.1246_1249del
  • NM_001323987.1:c.136_139del
  • NM_001323988.1:c.136_139del
  • NM_001323989.1:c.136_139del
  • NM_001323990.1:c.136_139del
  • NM_001323991.1:c.136_139del
  • NM_001323992.1:c.136_139del
  • NM_001323993.1:c.136_139del
  • NM_001323994.1:c.136_139del
  • NM_001323995.1:c.136_139del
  • NM_001323996.1:c.136_139del
  • NM_001323997.1:c.136_139del
  • NM_001323998.1:c.136_139del
  • NM_001323999.1:c.136_139del
  • NM_001324000.1:c.136_139del
  • NM_001324001.1:c.136_139del
  • NM_001324002.1:c.136_139del
  • NM_001324003.1:c.136_139del
  • NM_001324004.1:c.136_139del
  • NM_001324005.1:c.136_139del
  • NM_001324006.1:c.-262_-259del
  • NM_001324007.1:c.-262_-259del
  • NM_001324008.1:c.-262_-259del
  • NM_001324009.1:c.-262_-259del
  • NM_001324010.1:c.-61+11995_-61+11998del
  • NM_001324011.1:c.136_139del
  • NM_001324012.1:c.-58+11995_-58+11998del
  • NM_001324013.1:c.-137_-134del
  • NM_001903.2:c.1246_1249delGTTA
  • NM_001903.5:c.1246_1249delMANE SELECT
  • NP_001277236.1:p.Val416fs
  • NP_001277238.1:p.Val313fs
  • NP_001277239.1:p.Val293fs
  • NP_001277241.1:p.Val46fs
  • NP_001310911.1:p.Val416fs
  • NP_001310912.1:p.Val416fs
  • NP_001310913.1:p.Val416fs
  • NP_001310914.1:p.Val416fs
  • NP_001310915.1:p.Val416fs
  • NP_001310916.1:p.Val46fs
  • NP_001310917.1:p.Val46fs
  • NP_001310918.1:p.Val46fs
  • NP_001310919.1:p.Val46fs
  • NP_001310920.1:p.Val46fs
  • NP_001310921.1:p.Val46fs
  • NP_001310922.1:p.Val46fs
  • NP_001310923.1:p.Val46fs
  • NP_001310924.1:p.Val46fs
  • NP_001310925.1:p.Val46fs
  • NP_001310926.1:p.Val46fs
  • NP_001310927.1:p.Val46fs
  • NP_001310928.1:p.Val46fs
  • NP_001310929.1:p.Val46fs
  • NP_001310930.1:p.Val46fs
  • NP_001310931.1:p.Val46fs
  • NP_001310932.1:p.Val46fs
  • NP_001310933.1:p.Val46fs
  • NP_001310934.1:p.Val46fs
  • NP_001310940.1:p.Val46fs
  • NP_001894.2:p.Val416fs
  • NC_000005.9:g.138223280_138223283del
  • NC_000005.9:g.138223281_138223284del
  • NM_001903.3:c.1246_1249del
Protein change:
V293fs
Links:
dbSNP: rs1426385729
NCBI 1000 Genomes Browser:
rs1426385729
Molecular consequence:
  • NM_001324006.1:c.-262_-259del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001324007.1:c.-262_-259del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001324008.1:c.-262_-259del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001324009.1:c.-262_-259del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001324013.1:c.-137_-134del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001290307.3:c.1246_1249del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001290309.3:c.937_940del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001290310.3:c.877_880del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001290312.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323982.2:c.1246_1249del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323983.1:c.1246_1249del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323984.2:c.1246_1249del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323985.2:c.1246_1249del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323986.2:c.1246_1249del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323987.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323988.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323989.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323990.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323991.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323992.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323993.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323994.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323995.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323996.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323997.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323998.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323999.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001324000.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001324001.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001324002.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001324003.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001324004.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001324005.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001324011.1:c.136_139del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001903.5:c.1246_1249del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001324010.1:c.-61+11995_-61+11998del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001324012.1:c.-58+11995_-58+11998del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV001219197Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 20, 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001219197.5

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

Description

The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in CTNNA1 cause disease. 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. This variant has not been reported in the literature in individuals with CTNNA1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Val416Argfs*14) in the CTNNA1 gene. It is expected to result in an absent or disrupted protein product.

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

Last Updated: May 1, 2024