NM_000038.6(APC):c.7678C>T (p.Arg2560Ter) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 29, 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:: RCV001026699.11

Allele description [Variation Report for NM_000038.6(APC):c.7678C>T (p.Arg2560Ter)]

NM_000038.6(APC):c.7678C>T (p.Arg2560Ter)

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.7678C>T (p.Arg2560Ter)

HGVS:

NC_000005.10:g.112843272C>T
NG_008481.4:g.155752C>T
NM_000038.6:c.7678C>TMANE SELECT
NM_001127510.3:c.7678C>T
NM_001127511.3:c.7624C>T
NM_001354895.2:c.7678C>T
NM_001354896.2:c.7732C>T
NM_001354897.2:c.7708C>T
NM_001354898.2:c.7603C>T
NM_001354899.2:c.7594C>T
NM_001354900.2:c.7555C>T
NM_001354901.2:c.7501C>T
NM_001354902.2:c.7405C>T
NM_001354903.2:c.7375C>T
NM_001354904.2:c.7300C>T
NM_001354905.2:c.7198C>T
NM_001354906.2:c.6829C>T
NP_000029.2:p.Arg2560Ter
NP_001120982.1:p.Arg2560Ter
NP_001120983.2:p.Arg2542Ter
NP_001341824.1:p.Arg2560Ter
NP_001341825.1:p.Arg2578Ter
NP_001341826.1:p.Arg2570Ter
NP_001341827.1:p.Arg2535Ter
NP_001341828.1:p.Arg2532Ter
NP_001341829.1:p.Arg2519Ter
NP_001341830.1:p.Arg2501Ter
NP_001341831.1:p.Arg2469Ter
NP_001341832.1:p.Arg2459Ter
NP_001341833.1:p.Arg2434Ter
NP_001341834.1:p.Arg2400Ter
NP_001341835.1:p.Arg2277Ter
LRG_130:g.155752C>T
NC_000005.9:g.112178969C>T
NM_000038.5:c.7678C>T

Protein change:

R2277*

Links:

dbSNP: rs1580685528

NCBI 1000 Genomes Browser:

rs1580685528

Molecular consequence:

NM_000038.6:c.7678C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001127510.3:c.7678C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001127511.3:c.7624C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354895.2:c.7678C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354896.2:c.7732C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354897.2:c.7708C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354898.2:c.7603C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354899.2:c.7594C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354900.2:c.7555C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354901.2:c.7501C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354902.2:c.7405C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354903.2:c.7375C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354904.2:c.7300C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354905.2:c.7198C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354906.2:c.6829C>T - nonsense - [Sequence Ontology: SO:0001587]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001189129	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Feb 29, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001189129

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Feb 29, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV001189129.4

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

Description

The p.R2560* pathogenic mutation (also known as c.7678C>T), located in coding exon 15 of the APC gene, results from a C to T substitution at nucleotide position 7678. This changes the amino acid from an arginine to a stop codon within coding exon 15. This alteration has been observed multiple individuals with a personal and/or family history that is consistent with attenuated FAP (Ambry internal data). This alteration is expected to result in loss of function by premature protein truncation. As such, this alteration is interpreted as a disease-causing mutation.

#	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

Last Updated: Oct 26, 2024

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