NM_000038.6(APC):c.6019T>C (p.Tyr2007His) AND not specified

Germline classification:: Conflicting classifications of pathogenicity (3 submissions)
Last evaluated:: Mar 4, 2025
Review status:: criteria provided, conflicting classifications

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:: RCV000855566.20

Allele description [Variation Report for NM_000038.6(APC):c.6019T>C (p.Tyr2007His)]

NM_000038.6(APC):c.6019T>C (p.Tyr2007His)

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.6019T>C (p.Tyr2007His)

HGVS:

NC_000005.10:g.112841613T>C
NG_008481.4:g.154093T>C
NM_000038.6:c.6019T>CMANE SELECT
NM_001127510.3:c.6019T>C
NM_001127511.3:c.5965T>C
NM_001354895.2:c.6019T>C
NM_001354896.2:c.6073T>C
NM_001354897.2:c.6049T>C
NM_001354898.2:c.5944T>C
NM_001354899.2:c.5935T>C
NM_001354900.2:c.5896T>C
NM_001354901.2:c.5842T>C
NM_001354902.2:c.5746T>C
NM_001354903.2:c.5716T>C
NM_001354904.2:c.5641T>C
NM_001354905.2:c.5539T>C
NM_001354906.2:c.5170T>C
NP_000029.2:p.Tyr2007His
NP_001120982.1:p.Tyr2007His
NP_001120983.2:p.Tyr1989His
NP_001341824.1:p.Tyr2007His
NP_001341825.1:p.Tyr2025His
NP_001341826.1:p.Tyr2017His
NP_001341827.1:p.Tyr1982His
NP_001341828.1:p.Tyr1979His
NP_001341829.1:p.Tyr1966His
NP_001341830.1:p.Tyr1948His
NP_001341831.1:p.Tyr1916His
NP_001341832.1:p.Tyr1906His
NP_001341833.1:p.Tyr1881His
NP_001341834.1:p.Tyr1847His
NP_001341835.1:p.Tyr1724His
LRG_130t1:c.6019T>C
LRG_130:g.154093T>C
NC_000005.9:g.112177310T>C
NM_000038.4:c.6019T>C
NM_000038.5:c.6019T>C

Protein change:

Y1724H

Links:

dbSNP: rs745811356

Molecular consequence:

NM_000038.6:c.6019T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.6019T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.5965T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.6019T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.6073T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.6049T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.5944T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.5935T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.5896T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.5842T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.5746T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.5716T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.5641T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.5539T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.5170T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

Clear Turn Off Turn On

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
SCV000694088	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Feb 7, 2022)	germline	clinical testing	Citation Link,
SCV002550637	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Mar 4, 2025)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV006106028	Laboratory of Genetics, Children's Clinical University Hospital Latvia	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Feb 16, 2025)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000694088

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Feb 7, 2022)

germline

clinical testing

Citation Link,

SCV002550637

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Mar 4, 2025)

germline

clinical testing

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

SCV006106028

Laboratory of Genetics, Children's Clinical University Hospital Latvia

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Feb 16, 2025)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000694088.3

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

Description

Variant summary: APC c.6019T>C (p.Tyr2007His) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.8e-05 in 250120 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.6019T>C in individuals affected with Familial Adenomatous Polyposis and no experimental evidence demonstrating its impact on protein function have been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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 Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, SCV002550637.7

#	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 Laboratory of Genetics, Children's Clinical University Hospital Latvia, SCV006106028.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 12, 2026

ClinVar

Relating variation to medicine