NM_000038.6(APC):c.259C>T (p.Leu87=) AND not provided

Clinical significance:Benign/Likely benign (Last evaluated: May 5, 2021)

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]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000524797GeneDxcriteria provided, single submitter
Likely benign
(May 5, 2021)
germlineclinical testing

Citation Link,

SCV001133312Quest Diagnostics Nichols Institute San Juan Capistranocriteria provided, single submitter
(Feb 14, 2019)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing



A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

Details of each submission

From GeneDx, SCV000524797.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001133312.1

#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: Dec 4, 2021

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