NM_002528.7(NTHL1):c.332_333del (p.Cys110_Tyr111insTer) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 22, 2023
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:: RCV003575192.2

Allele description [Variation Report for NM_002528.7(NTHL1):c.332_333del (p.Cys110_Tyr111insTer)]

NM_002528.7(NTHL1):c.332_333del (p.Cys110_Tyr111insTer)

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.332_333del (p.Cys110_Tyr111insTer)

HGVS:

NC_000016.10:g.2046150_2046151del
NG_005895.1:g.1845_1846del
NG_008412.1:g.6717_6718del
NM_001318193.2:c.332_333del
NM_001318194.2:c.24+130_24+131del
NM_002528.7:c.332_333delMANE SELECT
NP_001305122.2:p.Cys110_Tyr111insTer
NP_002519.2:p.Cys110_Tyr111insTer
LRG_1366t1:c.332_333del
LRG_1366:g.6717_6718del
LRG_1366p1:p.Cys110_Tyr111insTer
LRG_487:g.1845_1846del
NC_000016.9:g.2096150_2096151del
NC_000016.9:g.2096151_2096152del

Molecular consequence:

NM_001318194.2:c.24+130_24+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001318193.2:c.332_333del - nonsense - [Sequence Ontology: SO:0001587]
NM_002528.7:c.332_333del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004366981	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 22, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 25938944, 26559593, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004366981

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 22, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

A germline homozygous mutation in the base-excision repair gene NTHL1 causes adenomatous polyposis and colorectal cancer.

Weren RD, Ligtenberg MJ, Kets CM, de Voer RM, Verwiel ET, Spruijt L, van Zelst-Stams WA, Jongmans MC, Gilissen C, Hehir-Kwa JY, Hoischen A, Shendure J, Boyle EA, Kamping EJ, Nagtegaal ID, Tops BB, Nagengast FM, Geurts van Kessel A, van Krieken JH, Kuiper RP, Hoogerbrugge N.

Nat Genet. 2015 Jun;47(6):668-71. doi: 10.1038/ng.3287. Epub 2015 May 4.

PubMed [citation]

PMID:: 25938944

Biallelic NTHL1 Mutations in a Woman with Multiple Primary Tumors.

Rivera B, Castellsagué E, Bah I, van Kempen LC, Foulkes WD.

N Engl J Med. 2015 Nov 12;373(20):1985-6. doi: 10.1056/NEJMc1506878. Erratum in: N Engl J Med. 2015 Dec 17;373(25):e33. doi: 10.1056/NEJMx150043.

PubMed [citation]

PMID:: 26559593

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004366981.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Tyr119*) in the NTHL1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NTHL1 are known to be pathogenic (PMID: 25938944, 26559593). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with NTHL1-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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: Sep 29, 2024

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