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NM_000038.6(APC):c.3029G>A (p.Ser1010Asn) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Dec 9, 2022
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:
RCV001018168.6

Allele description [Variation Report for NM_000038.6(APC):c.3029G>A (p.Ser1010Asn)]

NM_000038.6(APC):c.3029G>A (p.Ser1010Asn)

Gene:
APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q22.2
Genomic location:
Preferred name:
NM_000038.6(APC):c.3029G>A (p.Ser1010Asn)
HGVS:
  • NC_000005.10:g.112838623G>A
  • NG_008481.4:g.151103G>A
  • NM_000038.6:c.3029G>AMANE SELECT
  • NM_001127510.3:c.3029G>A
  • NM_001127511.3:c.2975G>A
  • NM_001354895.2:c.3029G>A
  • NM_001354896.2:c.3083G>A
  • NM_001354897.2:c.3059G>A
  • NM_001354898.2:c.2954G>A
  • NM_001354899.2:c.2945G>A
  • NM_001354900.2:c.2906G>A
  • NM_001354901.2:c.2852G>A
  • NM_001354902.2:c.2756G>A
  • NM_001354903.2:c.2726G>A
  • NM_001354904.2:c.2651G>A
  • NM_001354905.2:c.2549G>A
  • NM_001354906.2:c.2180G>A
  • NP_000029.2:p.Ser1010Asn
  • NP_001120982.1:p.Ser1010Asn
  • NP_001120983.2:p.Ser992Asn
  • NP_001341824.1:p.Ser1010Asn
  • NP_001341825.1:p.Ser1028Asn
  • NP_001341826.1:p.Ser1020Asn
  • NP_001341827.1:p.Ser985Asn
  • NP_001341828.1:p.Ser982Asn
  • NP_001341829.1:p.Ser969Asn
  • NP_001341830.1:p.Ser951Asn
  • NP_001341831.1:p.Ser919Asn
  • NP_001341832.1:p.Ser909Asn
  • NP_001341833.1:p.Ser884Asn
  • NP_001341834.1:p.Ser850Asn
  • NP_001341835.1:p.Ser727Asn
  • LRG_130:g.151103G>A
  • NC_000005.9:g.112174320G>A
  • NM_000038.5:c.3029G>A
Protein change:
S1010N
Links:
dbSNP: rs864622584
NCBI 1000 Genomes Browser:
rs864622584
Molecular consequence:
  • NM_000038.6:c.3029G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127510.3:c.3029G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127511.3:c.2975G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354895.2:c.3029G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354896.2:c.3083G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354897.2:c.3059G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354898.2:c.2954G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354899.2:c.2945G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354900.2:c.2906G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354901.2:c.2852G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354902.2:c.2756G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354903.2:c.2726G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354904.2:c.2651G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354905.2:c.2549G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354906.2:c.2180G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001179364Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Mar 18, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV001736037Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Dec 9, 2022) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Prevalence of the Y165C, G382D and 1395delGGA germline mutations of the MYH gene in Italian patients with adenomatous polyposis coli and colorectal adenomas.

Gismondi V, Meta M, Bonelli L, Radice P, Sala P, Bertario L, Viel A, Fornasarig M, Arrigoni A, Gentile M, Ponz de Leon M, Anselmi L, Mareni C, Bruzzi P, Varesco L.

Int J Cancer. 2004 May 1;109(5):680-4.

PubMed [citation]
PMID:
14999774

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Ambry Genetics, SCV001179364.4

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

Description

The p.S1010N variant (also known as c.3029G>A), located in coding exon 15 of the APC gene, results from a G to A substitution at nucleotide position 3029. The serine at codon 1010 is replaced by asparagine, an amino acid with highly similar properties. This alteration was reported in a 61-year-old individual with eight adenomas (Gismondi V et al. Int. J. Cancer 2004 May;109(5):680-4). This amino acid position is highly conserved in available vertebrate species. In addition, in silico predictors for this gene do not accurately predict pathogenicity. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

From Color Diagnostics, LLC DBA Color Health, SCV001736037.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This missense variant replaces serine with asparagine at codon 1010 of the APC protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with colorectal adenomas (PMID: 14999774). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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

Last Updated: May 1, 2024