NM_000038.6(APC):c.7793C>G (p.Thr2598Ser) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 24, 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:: RCV004036000.1

Allele description [Variation Report for NM_000038.6(APC):c.7793C>G (p.Thr2598Ser)]

NM_000038.6(APC):c.7793C>G (p.Thr2598Ser)

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.7793C>G (p.Thr2598Ser)

HGVS:

NC_000005.10:g.112843387C>G
NG_008481.4:g.155867C>G
NM_000038.5:c.7793C>G
NM_000038.6:c.7793C>GMANE SELECT
NM_001127510.3:c.7793C>G
NM_001127511.3:c.7739C>G
NM_001354895.2:c.7793C>G
NM_001354896.2:c.7847C>G
NM_001354897.2:c.7823C>G
NM_001354898.2:c.7718C>G
NM_001354899.2:c.7709C>G
NM_001354900.2:c.7670C>G
NM_001354901.2:c.7616C>G
NM_001354902.2:c.7520C>G
NM_001354903.2:c.7490C>G
NM_001354904.2:c.7415C>G
NM_001354905.2:c.7313C>G
NM_001354906.2:c.6944C>G
NP_000029.2:p.Thr2598Ser
NP_001120982.1:p.Thr2598Ser
NP_001120983.2:p.Thr2580Ser
NP_001341824.1:p.Thr2598Ser
NP_001341825.1:p.Thr2616Ser
NP_001341826.1:p.Thr2608Ser
NP_001341827.1:p.Thr2573Ser
NP_001341828.1:p.Thr2570Ser
NP_001341829.1:p.Thr2557Ser
NP_001341830.1:p.Thr2539Ser
NP_001341831.1:p.Thr2507Ser
NP_001341832.1:p.Thr2497Ser
NP_001341833.1:p.Thr2472Ser
NP_001341834.1:p.Thr2438Ser
NP_001341835.1:p.Thr2315Ser
LRG_130:g.155867C>G
NC_000005.9:g.112179084C>G

Protein change:

T2315S

Links:

dbSNP: rs747339588

NCBI 1000 Genomes Browser:

rs747339588

Molecular consequence:

NM_000038.6:c.7793C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7793C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7739C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7793C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7847C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7823C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7718C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7709C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7670C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7616C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7520C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7490C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7415C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7313C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6944C>G - 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

Recent activity

Clear Turn Off Turn On

PREDICTED: LOW QUALITY PROTEIN: NAC domain-containing protein 2-like [Cucumis me...
PREDICTED: LOW QUALITY PROTEIN: NAC domain-containing protein 2-like [Cucumis melo]
gi|659086936|ref|XP_008444188.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005035357	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Dec 24, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005035357

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Dec 24, 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, SCV005035357.1

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

Description

The p.T2598S variant (also known as c.7793C>G), located in coding exon 15 of the APC gene, results from a C to G substitution at nucleotide position 7793. The threonine at codon 2598 is replaced by serine, an amino acid with similar 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: Nov 3, 2024

ClinVar

Relating variation to medicine