NM_002528.7(NTHL1):c.832G>A (p.Gly278Ser) AND Familial adenomatous polyposis 3

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Feb 29, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000767389.6

Allele description [Variation Report for NM_002528.7(NTHL1):c.832G>A (p.Gly278Ser)]

NM_002528.7(NTHL1):c.832G>A (p.Gly278Ser)

Gene:

NTHL1:nth like DNA glycosylase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_002528.7(NTHL1):c.832G>A (p.Gly278Ser)

HGVS:

NC_000016.10:g.2040007C>T
NG_008412.1:g.12860G>A
NG_047104.1:g.18140C>T
NM_001318193.2:c.661G>A
NM_001318194.2:c.502G>A
NM_002528.7:c.832G>AMANE SELECT
NP_001305122.2:p.Gly221Ser
NP_001305123.1:p.Gly168Ser
NP_002519.2:p.Gly278Ser
LRG_1366t1:c.832G>A
LRG_1366:g.12860G>A
LRG_1366p1:p.Gly278Ser
NC_000016.9:g.2090008C>T
NM_002528.5:c.856G>A
NM_002528.6:c.856G>A

Protein change:

G168S

Links:

dbSNP: rs139309757

NCBI 1000 Genomes Browser:

rs139309757

Molecular consequence:

NM_001318193.2:c.661G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318194.2:c.502G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002528.7:c.832G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Familial adenomatous polyposis 3
Synonyms:: NTHL1-Related Adenomatous Polyposis and Colorectal Cancer; NTHL1-related attenuated familial adenomatous polyposis
Identifiers:: MONDO: MONDO:0014630; MedGen: C4225157; Orphanet: 220460; OMIM: 616415

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000844934	Molecular Oncology Laboratory, Hospital Clínico San Carlos	no assertion criteria provided (ACMG Guidelines, 2015)	Uncertain significance (Jun 1, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001367669	Centre for Mendelian Genomics, University Medical Centre Ljubljana	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 4, 2018)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005053724	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 29, 2024)	unknown	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

SCV000844934

Molecular Oncology Laboratory, Hospital Clínico San Carlos

no assertion criteria provided

(ACMG Guidelines, 2015)

Uncertain significance
(Jun 1, 2018)

germline

clinical testing

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

SCV001367669

Centre for Mendelian Genomics, University Medical Centre Ljubljana

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 4, 2018)

unknown

clinical testing

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

SCV005053724

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 29, 2024)

unknown

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	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	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 Molecular Oncology Laboratory, Hospital Clínico San Carlos, SCV000844934.1

#	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

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001367669.2

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

Description

This variant was classified as: Uncertain significance. The available evidence on this variant's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: PP3.

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

From Baylor Genetics, SCV005053724.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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