NM_000038.6(APC):c.7813C>A (p.Gln2605Lys) AND Familial adenomatous polyposis 1

delete

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 27, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003742891.1

Allele description

NM_000038.6(APC):c.7813C>A (p.Gln2605Lys)

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.7813C>A (p.Gln2605Lys)

HGVS:

NC_000005.10:g.112843407C>A
NG_008481.4:g.155887C>A
NM_000038.6:c.7813C>AMANE SELECT
NM_001127510.3:c.7813C>A
NM_001127511.3:c.7759C>A
NM_001354895.2:c.7813C>A
NM_001354896.2:c.7867C>A
NM_001354897.2:c.7843C>A
NM_001354898.2:c.7738C>A
NM_001354899.2:c.7729C>A
NM_001354900.2:c.7690C>A
NM_001354901.2:c.7636C>A
NM_001354902.2:c.7540C>A
NM_001354903.2:c.7510C>A
NM_001354904.2:c.7435C>A
NM_001354905.2:c.7333C>A
NM_001354906.2:c.6964C>A
NM_001407446.1:c.7897C>A
NM_001407447.1:c.7867C>A
NM_001407448.1:c.7867C>A
NM_001407449.1:c.7867C>A
NM_001407450.1:c.7813C>A
NM_001407451.1:c.7792C>A
NM_001407452.1:c.7783C>A
NM_001407453.1:c.7636C>A
NM_001407454.1:c.7564C>A
NM_001407455.1:c.7564C>A
NM_001407456.1:c.7564C>A
NM_001407457.1:c.7564C>A
NM_001407458.1:c.7510C>A
NM_001407459.1:c.7510C>A
NM_001407460.1:c.7510C>A
NM_001407467.1:c.7426C>A
NM_001407469.1:c.7426C>A
NM_001407470.1:c.6964C>A
NM_001407471.1:c.6661C>A
NM_001407472.1:c.6661C>A
NP_000029.2:p.Gln2605Lys
NP_000029.2:p.Gln2605Lys
NP_001120982.1:p.Gln2605Lys
NP_001120982.1:p.Gln2605Lys
NP_001120983.1:p.Gln2605Lys
NP_001120983.2:p.Gln2587Lys
NP_001341824.1:p.Gln2605Lys
NP_001341825.1:p.Gln2623Lys
NP_001341826.1:p.Gln2615Lys
NP_001341827.1:p.Gln2580Lys
NP_001341828.1:p.Gln2577Lys
NP_001341829.1:p.Gln2564Lys
NP_001341830.1:p.Gln2546Lys
NP_001341831.1:p.Gln2514Lys
NP_001341832.1:p.Gln2504Lys
NP_001341833.1:p.Gln2479Lys
NP_001341834.1:p.Gln2445Lys
NP_001341835.1:p.Gln2322Lys
NP_001394375.1:p.Gln2633Lys
NP_001394376.1:p.Gln2623Lys
NP_001394377.1:p.Gln2623Lys
NP_001394378.1:p.Gln2623Lys
NP_001394379.1:p.Gln2605Lys
NP_001394380.1:p.Gln2598Lys
NP_001394381.1:p.Gln2595Lys
NP_001394382.1:p.Gln2546Lys
NP_001394383.1:p.Gln2522Lys
NP_001394384.1:p.Gln2522Lys
NP_001394385.1:p.Gln2522Lys
NP_001394386.1:p.Gln2522Lys
NP_001394387.1:p.Gln2504Lys
NP_001394388.1:p.Gln2504Lys
NP_001394389.1:p.Gln2504Lys
NP_001394396.1:p.Gln2476Lys
NP_001394398.1:p.Gln2476Lys
NP_001394399.1:p.Gln2322Lys
NP_001394400.1:p.Gln2221Lys
NP_001394401.1:p.Gln2221Lys
LRG_130t1:c.7813C>A
LRG_130t2:c.7813C>A
LRG_130t3:c.7813C>A
LRG_130:g.155887C>A
LRG_130p1:p.Gln2605Lys
LRG_130p2:p.Gln2605Lys
LRG_130p3:p.Gln2605Lys
NC_000005.9:g.112179104C>A
NM_000038.4:c.7813C>A
NM_001127510.1:c.7813C>A
NM_001127511.1:c.7813C>A
NR_176365.1:n.7648C>A
NR_176366.1:n.8067C>A

Protein change:

Q2221K

Molecular consequence:

NM_000038.6:c.7813C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7813C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7759C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7813C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7867C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7843C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7738C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7729C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7690C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7636C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7540C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7510C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7435C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7333C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6964C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407446.1:c.7897C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407447.1:c.7867C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407448.1:c.7867C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407449.1:c.7867C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407450.1:c.7813C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407451.1:c.7792C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407452.1:c.7783C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407453.1:c.7636C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407454.1:c.7564C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407455.1:c.7564C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407456.1:c.7564C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407457.1:c.7564C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407458.1:c.7510C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407459.1:c.7510C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407460.1:c.7510C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407467.1:c.7426C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407469.1:c.7426C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407470.1:c.6964C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407471.1:c.6661C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407472.1:c.6661C>A - missense variant - [Sequence Ontology: SO:0001583]

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

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DNA replication complex GINS protein PSF3 isoform b [Homo sapiens]
DNA replication complex GINS protein PSF3 isoform b [Homo sapiens]
gi|21362088|ref|NP_073607.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003199650	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 27, 2022)	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

SCV003199650

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 27, 2022)

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	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 Invitae, SCV003199650.2

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with APC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamine, which is neutral and polar, with lysine, which is basic and polar, at codon 2605 of the APC protein (p.Gln2605Lys).

#	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: Jun 9, 2024

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