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NM_000038.6(APC):c.7739C>T (p.Ser2580Phe) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 14, 2024
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:
RCV002397619.10

Allele description [Variation Report for NM_000038.6(APC):c.7739C>T (p.Ser2580Phe)]

NM_000038.6(APC):c.7739C>T (p.Ser2580Phe)

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.7739C>T (p.Ser2580Phe)
HGVS:
  • NC_000005.10:g.112843333C>T
  • NG_008481.4:g.155813C>T
  • NM_000038.6:c.7739C>TMANE SELECT
  • NM_001127510.3:c.7739C>T
  • NM_001127511.3:c.7685C>T
  • NM_001354895.2:c.7739C>T
  • NM_001354896.2:c.7793C>T
  • NM_001354897.2:c.7769C>T
  • NM_001354898.2:c.7664C>T
  • NM_001354899.2:c.7655C>T
  • NM_001354900.2:c.7616C>T
  • NM_001354901.2:c.7562C>T
  • NM_001354902.2:c.7466C>T
  • NM_001354903.2:c.7436C>T
  • NM_001354904.2:c.7361C>T
  • NM_001354905.2:c.7259C>T
  • NM_001354906.2:c.6890C>T
  • NP_000029.2:p.Ser2580Phe
  • NP_001120982.1:p.Ser2580Phe
  • NP_001120983.2:p.Ser2562Phe
  • NP_001341824.1:p.Ser2580Phe
  • NP_001341825.1:p.Ser2598Phe
  • NP_001341826.1:p.Ser2590Phe
  • NP_001341827.1:p.Ser2555Phe
  • NP_001341828.1:p.Ser2552Phe
  • NP_001341829.1:p.Ser2539Phe
  • NP_001341830.1:p.Ser2521Phe
  • NP_001341831.1:p.Ser2489Phe
  • NP_001341832.1:p.Ser2479Phe
  • NP_001341833.1:p.Ser2454Phe
  • NP_001341834.1:p.Ser2420Phe
  • NP_001341835.1:p.Ser2297Phe
  • LRG_130:g.155813C>T
  • NC_000005.9:g.112179030C>T
  • NM_000038.5:c.7739C>T
Protein change:
S2297F
Links:
dbSNP: rs1012830859
NCBI 1000 Genomes Browser:
rs1012830859
Molecular consequence:
  • NM_000038.6:c.7739C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127510.3:c.7739C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127511.3:c.7685C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354895.2:c.7739C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354896.2:c.7793C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354897.2:c.7769C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354898.2:c.7664C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354899.2:c.7655C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354900.2:c.7616C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354901.2:c.7562C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354902.2:c.7466C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354903.2:c.7436C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354904.2:c.7361C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354905.2:c.7259C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354906.2:c.6890C>T - 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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002669345Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Jun 14, 2024) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV002669345.3

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

Description

The p.S2580F variant (also known as c.7739C>T), located in coding exon 15 of the APC gene, results from a C to T substitution at nucleotide position 7739. The serine at codon 2580 is replaced by phenylalanine, an amino acid with highly dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, in silico predictors for this gene do not accurately predict pathogenicity. Missense alterations in APC are not a common cause of disease (Spier I et al. Genet Med. 2024 Feb;26(2):100992). Based on the available evidence, the clinical significance of this variant remains unclear.

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

Last Updated: Sep 29, 2024