NM_004655.4(AXIN2):c.1168A>G (p.Ser390Gly) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely benign (4 submissions)
Last evaluated:: Oct 1, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000656767.25

Allele description

NM_004655.4(AXIN2):c.1168A>G (p.Ser390Gly)

Gene:

AXIN2:axin 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q24.1

Genomic location:

Preferred name:

NM_004655.4(AXIN2):c.1168A>G (p.Ser390Gly)

Other names:

p.S390G:AGC>GGC

HGVS:

NC_000017.11:g.65538235T>C
NG_012142.1:g.28388A>G
NM_001363813.1:c.1168A>G
NM_004655.4:c.1168A>GMANE SELECT
NP_001350742.1:p.Ser390Gly
NP_004646.3:p.Ser390Gly
LRG_296t1:c.1168A>G
LRG_296:g.28388A>G
NC_000017.10:g.63534353T>C
NM_004655.3:c.1168A>G

Protein change:

S390G

Links:

dbSNP: rs139871607

NCBI 1000 Genomes Browser:

rs139871607

Molecular consequence:

NM_001363813.1:c.1168A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004655.4:c.1168A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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BioProject Links for Protein (Select 452849402) (1)
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Homo sapiens
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RefSeq annotation of the human reference genome assembly

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Xenopus laevis isolate BJE3547 p7e4 (p7e4) gene, partial cds
Xenopus laevis isolate BJE3547 p7e4 (p7e4) gene, partial cds
gi|749393514|gb|KP344480.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000149775	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Oct 29, 2020)	germline	clinical testing	Citation Link,
SCV001473952	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Likely benign (Jul 10, 2020)	germline	clinical testing	Citation Link,
SCV001553020	Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR) See additional submitters Franklin by Genoox	no assertion criteria provided	Likely benign	unknown	clinical testing
SCV002822420	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Oct 1, 2023)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	5	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000149775.16

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is associated with the following publications: (PMID: 27300758, 30374176)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001473952.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001553020.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The AXIN2 p.Ser390Gly variant was not identified in the literature nor was it identified in Cosmic. The variant was identified in dbSNP (ID: rs139871607) and ClinVar (classified as likely benign by Illumina, Invitae and the University of Washington Department of Laboratory Medicine and as uncertain significance by GeneDx, Mayo Clinic Genetic Testing Laboratories and the CSER_CC_NCGL; University of Washington Medical Center). The variant was also identified in control databases in 210 of 282220 chromosomes at a frequency of 0.000744 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 183 of 128706 chromosomes (freq: 0.001422), Other in 7 of 7206 chromosomes (freq: 0.000971), European (Finnish) in 8 of 25094 chromosomes (freq: 0.000319), African in 5 of 24886 chromosomes (freq: 0.000201) and Latino in 7 of 35408 chromosomes (freq: 0.000198), but was not observed in the Ashkenazi Jewish, East Asian or South Asian populations. The p.Ser390 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant also occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV002822420.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	5	not provided	not provided	clinical testing	not provided

Description

AXIN2: BP4

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		5	not provided	not provided	not provided

Last Updated: May 7, 2024

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