NM_002528.7(NTHL1):c.354G>A (p.Lys118=) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 29, 2020
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:: RCV002353066.2

Allele description [Variation Report for NM_002528.7(NTHL1):c.354G>A (p.Lys118=)]

NM_002528.7(NTHL1):c.354G>A (p.Lys118=)

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.354G>A (p.Lys118=)

HGVS:

NC_000016.10:g.2046128C>T
NG_005895.1:g.1823C>T
NG_008412.1:g.6739G>A
NM_001318193.2:c.354G>A
NM_001318194.2:c.24+152G>A
NM_002528.7:c.354G>AMANE SELECT
NP_001305122.2:p.Lys118=
NP_002519.2:p.Lys118=
LRG_1366t1:c.354G>A
LRG_1366:g.6739G>A
LRG_1366p1:p.Lys118=
LRG_487:g.1823C>T
NC_000016.9:g.2096129C>T
NM_002528.5:c.378G>A

Molecular consequence:

NM_001318194.2:c.24+152G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001318193.2:c.354G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_002528.7:c.354G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002622693	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Sep 29, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002622693

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Sep 29, 2020)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV002622693.2

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

Description

The c.378G>A variant (also known as p.K126K), located in coding exon 2 of the NTHL1 gene, results from a G to A substitution at nucleotide position 378. This nucleotide substitution does not change the lysine at codon 126. However, this change occurs in the last base pair of coding exon 2, which makes it likely to have some effect on normal mRNA splicing. This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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