NM_002528.7(NTHL1):c.680G>A (p.Gly227Asp) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 30, 2021
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:: RCV001816871.4

Allele description [Variation Report for NM_002528.7(NTHL1):c.680G>A (p.Gly227Asp)]

NM_002528.7(NTHL1):c.680G>A (p.Gly227Asp)

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.680G>A (p.Gly227Asp)

HGVS:

NC_000016.10:g.2043572C>T
NG_008412.1:g.9295G>A
NM_001318193.2:c.509G>A
NM_001318194.2:c.350G>A
NM_002528.7:c.680G>AMANE SELECT
NP_001305122.2:p.Gly170Asp
NP_001305123.1:p.Gly117Asp
NP_002519.2:p.Gly227Asp
LRG_1366t1:c.680G>A
LRG_1366:g.9295G>A
LRG_1366p1:p.Gly227Asp
NC_000016.9:g.2093573C>T
NM_002528.5:c.704G>A
NM_002528.6:c.704G>A

Protein change:

G117D

Links:

dbSNP: rs1055874267

NCBI 1000 Genomes Browser:

rs1055874267

Molecular consequence:

NM_001318193.2:c.509G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318194.2:c.350G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002528.7:c.680G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002071881	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 30, 2021)	germline	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

SCV002071881

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 30, 2021)

germline

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	germline	no	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 Genetic Services Laboratory, University of Chicago, SCV002071881.1

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

Description

DNA sequence analysis of the NTHL1 gene demonstrated a sequence change, c.680G>A, in exon 4 that results in an amino acid change, p.Gly227Asp. This sequence change does not appear to have been previously described in individuals with NTHL1-related disorders. This sequence change has been described in the gnomAD database in one individual which corresponds to a population frequency of 0.00041% (dbSNP rs1055874267). The p.Gly227Asp change affects a highly conserved amino acid residue located in a domain of the NTHL1 protein that is known to be functional. The p.Gly227Asp substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). Due to insufficient evidence and the lack of functional studies, the clinical significance of the p.Gly227Asp change remains unknown at this time.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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