NM_001127511.3(APC):c.130G>A (p.Ala44Thr) AND Familial adenomatous polyposis 1

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jan 22, 2024
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:: RCV000412427.22

Allele description [Variation Report for NM_001127511.3(APC):c.130G>A (p.Ala44Thr)]

NM_001127511.3(APC):c.130G>A (p.Ala44Thr)

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_001127511.3(APC):c.130G>A (p.Ala44Thr)

HGVS:

NC_000005.10:g.112707847G>A
NG_008481.4:g.20327G>A
NM_001127511.3:c.130G>A
NM_001354895.2:c.-54G>A
NM_001354897.2:c.130G>A
NM_001354902.2:c.130G>A
NM_001407446.1:c.130G>A
NM_001407447.1:c.-54G>A
NM_001407448.1:c.-19+198G>A
NM_001407450.1:c.-19+198G>A
NM_001407452.1:c.-54G>A
NM_001407453.1:c.-43+198G>A
NM_001407456.1:c.-54G>A
NM_001407457.1:c.-19+198G>A
NM_001407458.1:c.-19+198G>A
NM_001407460.1:c.-54G>A
NM_001407469.1:c.-54G>A
NM_001407470.1:c.-1089G>A
NM_001407472.1:c.-1089G>A
NP_001120983.2:p.Ala44Thr
NP_001341826.1:p.Ala44Thr
NP_001341831.1:p.Ala44Thr
NP_001394375.1:p.Ala44Thr
LRG_130t3:c.-54G>A
LRG_130:g.20327G>A
NC_000005.9:g.112043544G>A
NM_000038.5:c.-30097G>A
NM_001127511.1:c.-54G>A
NM_001127511.2:c.130G>A
NR_176366.1:n.350G>A

Protein change:

A44T

Links:

dbSNP: rs367773779

NCBI 1000 Genomes Browser:

rs367773779

Molecular consequence:

NM_001354895.2:c.-54G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407447.1:c.-54G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407452.1:c.-54G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407456.1:c.-54G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407460.1:c.-54G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407469.1:c.-54G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407470.1:c.-1089G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407472.1:c.-1089G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407448.1:c.-19+198G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407450.1:c.-19+198G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407453.1:c.-43+198G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407457.1:c.-19+198G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407458.1:c.-19+198G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001127511.3:c.130G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.130G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.130G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407446.1:c.130G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_176366.1:n.350G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Familial adenomatous polyposis 1 (FAP1)
Synonyms:: POLYPOSIS, ADENOMATOUS INTESTINAL; FAMILIAL ADENOMATOUS POLYPOSIS 1, ATTENUATED; APC-Associated Polyposis Conditions
Identifiers:: MONDO: MONDO:0021056; MedGen: C2713442; OMIM: 175100

Recent activity

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hypothetical protein THRCLA_07750 [Thraustotheca clavata]
hypothetical protein THRCLA_07750 [Thraustotheca clavata]
gi|1173947190|gb|OQR95574.1||gnl|WG S|THRCLA_07750.1

Protein
Gene Links for GEO Profiles (Select 124397762) (1)
Gene
EMC9 ER membrane protein complex subunit 9 [Homo sapiens]
EMC9 ER membrane protein complex subunit 9 [Homo sapiens]
Gene ID:51016

Gene
Gene Links for GEO Profiles (Select 90874457) (2)
Gene
Homologene neighbors for GEO Profiles (Select 74885162) (0)
GEO Profiles

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000488687	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Uncertain significance (May 25, 2016)	unknown	clinical testing	Counsyl Autosomal Dominant Disease Classification criteria (2015), Citation Link,
SCV000647295	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 22, 2024)	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

SCV000488687

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Uncertain significance
(May 25, 2016)

unknown

clinical testing

Counsyl Autosomal Dominant Disease Classification criteria (2015),

Citation Link,

SCV000647295

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 22, 2024)

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	unknown	unknown	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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Counsyl, SCV000488687.2

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000647295.8

#	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

Last Updated: Nov 10, 2024

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