NM_000038.6(APC):c.259C>T (p.Leu87=) AND Hereditary cancer-predisposing syndrome

Clinical significance:Benign/Likely benign (Last evaluated: May 28, 2016)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_000038.6(APC):c.259C>T (p.Leu87=)]

NM_000038.6(APC):c.259C>T (p.Leu87=)

APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000038.6(APC):c.259C>T (p.Leu87=)
  • NC_000005.10:g.112767227C>T
  • NG_008481.4:g.79707C>T
  • NM_000038.6:c.259C>TMANE SELECT
  • NM_001127510.3:c.259C>T
  • NM_001127511.3:c.289C>T
  • NM_001354895.2:c.259C>T
  • NM_001354896.2:c.259C>T
  • NM_001354897.2:c.289C>T
  • NM_001354898.2:c.184C>T
  • NM_001354899.2:c.259C>T
  • NM_001354900.2:c.82C>T
  • NM_001354901.2:c.82C>T
  • NM_001354902.2:c.289C>T
  • NM_001354903.2:c.259C>T
  • NM_001354904.2:c.184C>T
  • NM_001354905.2:c.82C>T
  • NM_001354906.2:c.-777C>T
  • NP_000029.2:p.Leu87=
  • NP_001120982.1:p.Leu87=
  • NP_001120983.2:p.Leu97=
  • NP_001341824.1:p.Leu87=
  • NP_001341825.1:p.Leu87=
  • NP_001341826.1:p.Leu97=
  • NP_001341827.1:p.Leu62=
  • NP_001341828.1:p.Leu87=
  • NP_001341829.1:p.Leu28=
  • NP_001341830.1:p.Leu28=
  • NP_001341831.1:p.Leu97=
  • NP_001341832.1:p.Leu87=
  • NP_001341833.1:p.Leu62=
  • NP_001341834.1:p.Leu28=
  • LRG_130:g.79707C>T
  • NC_000005.9:g.112102924C>T
  • NM_000038.5:c.259C>T
  • p.L87L
dbSNP: rs569640184
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001354906.2:c.-777C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000038.6:c.259C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127510.3:c.259C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127511.3:c.289C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354895.2:c.259C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354896.2:c.259C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354897.2:c.289C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354898.2:c.184C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354899.2:c.259C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354900.2:c.82C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354901.2:c.82C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354902.2:c.289C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354903.2:c.259C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354904.2:c.184C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354905.2:c.82C>T - synonymous variant - [Sequence Ontology: SO:0001819]


Hereditary cancer-predisposing syndrome
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
MONDO: MONDO:0015356; MedGen: C0027672

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000214081Ambry Geneticscriteria provided, single submitter
Likely benign
(Apr 21, 2015)
germlineclinical testing

Citation Link,

SCV000681538Color Health, Inccriteria provided, single submitter
(May 28, 2016)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing



Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

Details of each submission

From Ambry Genetics, SCV000214081.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided


This alteration is classified as likely benign based on a combination of the following: 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.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

From Color Health, Inc, SCV000681538.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 20, 2021

Support Center