NM_002528.7(NTHL1):c.491T>C (p.Leu164Pro) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 25, 2024
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:: RCV002336604.4

Allele description [Variation Report for NM_002528.7(NTHL1):c.491T>C (p.Leu164Pro)]

NM_002528.7(NTHL1):c.491T>C (p.Leu164Pro)

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.491T>C (p.Leu164Pro)

HGVS:

NC_000016.10:g.2044664A>G
NG_005895.1:g.359A>G
NG_008412.1:g.8203T>C
NM_001318193.2:c.355-938T>C
NM_001318194.2:c.161T>C
NM_002528.7:c.491T>CMANE SELECT
NP_001305123.1:p.Leu54Pro
NP_002519.2:p.Leu164Pro
LRG_1366t1:c.491T>C
LRG_1366:g.8203T>C
LRG_1366p1:p.Leu164Pro
LRG_487:g.359A>G
NC_000016.9:g.2094665A>G
NM_002528.5:c.515T>C
NM_002528.6:c.515T>C

Protein change:

L164P

Links:

dbSNP: rs1162857718

NCBI 1000 Genomes Browser:

rs1162857718

Molecular consequence:

NM_001318193.2:c.355-938T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001318194.2:c.161T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_002528.7:c.491T>C - missense variant - [Sequence Ontology: SO:0001583]

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
SCV002641348	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Apr 25, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002641348

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Apr 25, 2024)

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, SCV002641348.3

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

Description

The p.L172P variant (also known as c.515T>C), located in coding exon 3 of the NTHL1 gene, results from a T to C substitution at nucleotide position 515. The leucine at codon 172 is replaced by proline, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this variant 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: Oct 20, 2024

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