NM_002528.7(NTHL1):c.232del (p.Val78fs) AND Familial adenomatous polyposis 3

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Sep 21, 2023
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:: RCV003336244.3

Allele description [Variation Report for NM_002528.7(NTHL1):c.232del (p.Val78fs)]

NM_002528.7(NTHL1):c.232del (p.Val78fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_002528.7(NTHL1):c.232del (p.Val78fs)

HGVS:

NC_000016.10:g.2046250del
NG_005895.1:g.1945del
NG_008412.1:g.6617del
NM_001318193.2:c.232del
NM_001318194.2:c.24+30del
NM_002528.7:c.232delMANE SELECT
NP_001305122.2:p.Val78fs
NP_002519.2:p.Val78fs
LRG_1366t1:c.232del
LRG_1366:g.6617del
LRG_1366p1:p.Val78fs
LRG_487:g.1945del
NC_000016.9:g.2096251del
NC_000016.9:g.2096251del
NM_002528.5:c.256delG

Protein change:

V78fs

Links:

dbSNP: rs1314290585

NCBI 1000 Genomes Browser:

rs1314290585

Molecular consequence:

NM_001318193.2:c.232del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002528.7:c.232del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318194.2:c.24+30del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV004043856	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Apr 26, 2023)	unknown	clinical testing	Citation Link,
SCV004192120	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 21, 2023)	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

SCV004043856

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Pathogenic
(Apr 26, 2023)

unknown

clinical testing

Citation Link,

SCV004192120

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Sep 21, 2023)

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	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 Myriad Genetics, Inc., SCV004043856.2

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

Description

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.

#	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 Baylor Genetics, SCV004192120.1

#	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: Sep 29, 2024

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