NM_000038.6(APC):c.7743T>A (p.Ser2581Arg) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 16, 2023
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:: RCV003358454.2

Allele description [Variation Report for NM_000038.6(APC):c.7743T>A (p.Ser2581Arg)]

NM_000038.6(APC):c.7743T>A (p.Ser2581Arg)

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.7743T>A (p.Ser2581Arg)

HGVS:

NC_000005.10:g.112843337T>A
NG_008481.4:g.155817T>A
NM_000038.6:c.7743T>AMANE SELECT
NM_001127510.3:c.7743T>A
NM_001127511.3:c.7689T>A
NM_001354895.2:c.7743T>A
NM_001354896.2:c.7797T>A
NM_001354897.2:c.7773T>A
NM_001354898.2:c.7668T>A
NM_001354899.2:c.7659T>A
NM_001354900.2:c.7620T>A
NM_001354901.2:c.7566T>A
NM_001354902.2:c.7470T>A
NM_001354903.2:c.7440T>A
NM_001354904.2:c.7365T>A
NM_001354905.2:c.7263T>A
NM_001354906.2:c.6894T>A
NM_001407446.1:c.7827T>A
NM_001407447.1:c.7797T>A
NM_001407448.1:c.7797T>A
NM_001407449.1:c.7797T>A
NM_001407450.1:c.7743T>A
NM_001407451.1:c.7722T>A
NM_001407452.1:c.7713T>A
NM_001407453.1:c.7566T>A
NM_001407454.1:c.7494T>A
NM_001407455.1:c.7494T>A
NM_001407456.1:c.7494T>A
NM_001407457.1:c.7494T>A
NM_001407458.1:c.7440T>A
NM_001407459.1:c.7440T>A
NM_001407460.1:c.7440T>A
NM_001407467.1:c.7356T>A
NM_001407469.1:c.7356T>A
NM_001407470.1:c.6894T>A
NM_001407471.1:c.6591T>A
NM_001407472.1:c.6591T>A
NP_000029.2:p.Ser2581Arg
NP_000029.2:p.Ser2581Arg
NP_001120982.1:p.Ser2581Arg
NP_001120982.1:p.Ser2581Arg
NP_001120983.1:p.Ser2581Arg
NP_001120983.2:p.Ser2563Arg
NP_001341824.1:p.Ser2581Arg
NP_001341825.1:p.Ser2599Arg
NP_001341826.1:p.Ser2591Arg
NP_001341827.1:p.Ser2556Arg
NP_001341828.1:p.Ser2553Arg
NP_001341829.1:p.Ser2540Arg
NP_001341830.1:p.Ser2522Arg
NP_001341831.1:p.Ser2490Arg
NP_001341832.1:p.Ser2480Arg
NP_001341833.1:p.Ser2455Arg
NP_001341834.1:p.Ser2421Arg
NP_001341835.1:p.Ser2298Arg
NP_001394375.1:p.Ser2609Arg
NP_001394376.1:p.Ser2599Arg
NP_001394377.1:p.Ser2599Arg
NP_001394378.1:p.Ser2599Arg
NP_001394379.1:p.Ser2581Arg
NP_001394380.1:p.Ser2574Arg
NP_001394381.1:p.Ser2571Arg
NP_001394382.1:p.Ser2522Arg
NP_001394383.1:p.Ser2498Arg
NP_001394384.1:p.Ser2498Arg
NP_001394385.1:p.Ser2498Arg
NP_001394386.1:p.Ser2498Arg
NP_001394387.1:p.Ser2480Arg
NP_001394388.1:p.Ser2480Arg
NP_001394389.1:p.Ser2480Arg
NP_001394396.1:p.Ser2452Arg
NP_001394398.1:p.Ser2452Arg
NP_001394399.1:p.Ser2298Arg
NP_001394400.1:p.Ser2197Arg
NP_001394401.1:p.Ser2197Arg
LRG_130t1:c.7743T>A
LRG_130t2:c.7743T>A
LRG_130t3:c.7743T>A
LRG_130:g.155817T>A
LRG_130p1:p.Ser2581Arg
LRG_130p2:p.Ser2581Arg
LRG_130p3:p.Ser2581Arg
NC_000005.9:g.112179034T>A
NM_000038.4:c.7743T>A
NM_000038.5:c.7743T>A
NM_001127510.1:c.7743T>A
NM_001127511.1:c.7743T>A
NR_176365.1:n.7578T>A
NR_176366.1:n.7997T>A

Protein change:

S2197R

Molecular consequence:

NM_000038.6:c.7743T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7743T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7689T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7743T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7797T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7773T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7668T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7659T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7620T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7566T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7470T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7440T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7365T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7263T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6894T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407446.1:c.7827T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407447.1:c.7797T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407448.1:c.7797T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407449.1:c.7797T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407450.1:c.7743T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407451.1:c.7722T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407452.1:c.7713T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407453.1:c.7566T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407454.1:c.7494T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407455.1:c.7494T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407456.1:c.7494T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407457.1:c.7494T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407458.1:c.7440T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407459.1:c.7440T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407460.1:c.7440T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407467.1:c.7356T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407469.1:c.7356T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407470.1:c.6894T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407471.1:c.6591T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407472.1:c.6591T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_176365.1:n.7578T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176366.1:n.7997T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV004053862	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jun 16, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004053862

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jun 16, 2023)

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, SCV004053862.2

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

Description

The p.S2581R variant (also known as c.7743T>A), located in coding exon 15 of the APC gene, results from a T to A substitution at nucleotide position 7743. The serine at codon 2581 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is conserved. 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.

#	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: May 1, 2024

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