NM_000038.6(APC):c.5801C>T (p.Pro1934Leu) AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Apr 18, 2023
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:: RCV000159562.26

Allele description [Variation Report for NM_000038.6(APC):c.5801C>T (p.Pro1934Leu)]

NM_000038.6(APC):c.5801C>T (p.Pro1934Leu)

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.5801C>T (p.Pro1934Leu)

Other names:

p.P1934L:CCC>CTC

HGVS:

NC_000005.10:g.112841395C>T
NG_008481.4:g.153875C>T
NM_000038.6:c.5801C>TMANE SELECT
NM_001127510.3:c.5801C>T
NM_001127511.3:c.5747C>T
NM_001354895.2:c.5801C>T
NM_001354896.2:c.5855C>T
NM_001354897.2:c.5831C>T
NM_001354898.2:c.5726C>T
NM_001354899.2:c.5717C>T
NM_001354900.2:c.5678C>T
NM_001354901.2:c.5624C>T
NM_001354902.2:c.5528C>T
NM_001354903.2:c.5498C>T
NM_001354904.2:c.5423C>T
NM_001354905.2:c.5321C>T
NM_001354906.2:c.4952C>T
NP_000029.2:p.Pro1934Leu
NP_001120982.1:p.Pro1934Leu
NP_001120983.2:p.Pro1916Leu
NP_001341824.1:p.Pro1934Leu
NP_001341825.1:p.Pro1952Leu
NP_001341826.1:p.Pro1944Leu
NP_001341827.1:p.Pro1909Leu
NP_001341828.1:p.Pro1906Leu
NP_001341829.1:p.Pro1893Leu
NP_001341830.1:p.Pro1875Leu
NP_001341831.1:p.Pro1843Leu
NP_001341832.1:p.Pro1833Leu
NP_001341833.1:p.Pro1808Leu
NP_001341834.1:p.Pro1774Leu
NP_001341835.1:p.Pro1651Leu
LRG_130t1:c.5801C>T
LRG_130:g.153875C>T
NC_000005.9:g.112177092C>T
NM_000038.4:c.5801C>T
NM_000038.5:c.5801C>T
p.P1934L

Protein change:

P1651L

Links:

dbSNP: rs587780600

NCBI 1000 Genomes Browser:

rs587780600

Molecular consequence:

NM_000038.6:c.5801C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.5801C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.5747C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.5801C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.5855C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.5831C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.5726C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.5717C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.5678C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.5624C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.5528C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.5498C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.5423C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.5321C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.4952C>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000213581	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Benign (Jun 12, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 26580448, 26845104, 30267214 Citation Link,
SCV000681763	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 18, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002528010	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Likely benign (Dec 18, 2021)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000213581

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Benign
(Jun 12, 2020)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV000681763

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Apr 18, 2023)

germline

clinical testing

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

SCV002528010

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Likely benign
(Dec 18, 2021)

germline

curation

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, curation

Citations

PubMed

Germline Mutations in Predisposition Genes in Pediatric Cancer.

Zhang J, Walsh MF, Wu G, Edmonson MN, Gruber TA, Easton J, Hedges D, Ma X, Zhou X, Yergeau DA, Wilkinson MR, Vadodaria B, Chen X, McGee RB, Hines-Dowell S, Nuccio R, Quinn E, Shurtleff SA, Rusch M, Patel A, Becksfort JB, Wang S, et al.

N Engl J Med. 2015 Dec 10;373(24):2336-2346. doi: 10.1056/NEJMoa1508054. Epub 2015 Nov 18.

PubMed [citation]

PMID:: 26580448
PMCID:: PMC4734119

Improving performance of multigene panels for genomic analysis of cancer predisposition.

Shirts BH, Casadei S, Jacobson AL, Lee MK, Gulsuner S, Bennett RL, Miller M, Hall SA, Hampel H, Hisama FM, Naylor LV, Goetsch C, Leppig K, Tait JF, Scroggins SM, Turner EH, Livingston R, Salipante SJ, King MC, Walsh T, Pritchard CC.

Genet Med. 2016 Oct;18(10):974-81. doi: 10.1038/gim.2015.212. Epub 2016 Feb 4.

PubMed [citation]

PMID:: 26845104

See all PubMed Citations (4)

Details of each submission

From Ambry Genetics, SCV000213581.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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

From Color Diagnostics, LLC DBA Color Health, SCV000681763.6

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

#	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

From Sema4, Sema4, SCV002528010.1

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

#	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 8, 2024

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