NM_002528.7(NTHL1):c.139G>A (p.Val47Met) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Mar 15, 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:: RCV002255529.5

Allele description [Variation Report for NM_002528.7(NTHL1):c.139G>A (p.Val47Met)]

NM_002528.7(NTHL1):c.139G>A (p.Val47Met)

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.139G>A (p.Val47Met)

HGVS:

NC_000016.10:g.2046343C>T
NG_005895.1:g.2038C>T
NG_008412.1:g.6524G>A
NM_001318193.2:c.139G>A
NM_001318194.2:c.-40G>A
NM_002528.7:c.139G>AMANE SELECT
NP_001305122.2:p.Val47Met
NP_002519.2:p.Val47Met
LRG_1366t1:c.139G>A
LRG_1366:g.6524G>A
LRG_1366p1:p.Val47Met
LRG_487:g.2038C>T
NC_000016.9:g.2096344C>T
NM_002528.5:c.163G>A
NM_002528.6:c.163G>A

Protein change:

V47M

Links:

dbSNP: rs1210160367

NCBI 1000 Genomes Browser:

rs1210160367

Molecular consequence:

NM_001318194.2:c.-40G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001318193.2:c.139G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002528.7:c.139G>A - 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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Armillaria gallica strain FOD8_21 large subunit ribosomal RNA gene and intergenic spacer 1, partial sequence
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002528920	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Uncertain significance (Aug 19, 2021)	germline	curation	Citation Link,
SCV002703055	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Mar 15, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002528920

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Uncertain significance
(Aug 19, 2021)

germline

curation

Citation Link,

SCV002703055

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Mar 15, 2023)

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, curation

Details of each submission

From Sema4, Sema4, SCV002528920.1

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

#	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

From Ambry Genetics, SCV002703055.3

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

Description

The p.V55M variant (also known as c.163G>A), located in coding exon 2 of the NTHL1 gene, results from a G to A substitution at nucleotide position 163. The valine at codon 55 is replaced by methionine, an amino acid with highly similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. 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: Oct 13, 2024

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