NM_002528.7(NTHL1):c.319A>C (p.Thr107Pro) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 9, 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:: RCV001048419.7

Allele description

NM_002528.7(NTHL1):c.319A>C (p.Thr107Pro)

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.319A>C (p.Thr107Pro)

HGVS:

NC_000016.10:g.2046163T>G
NG_005895.1:g.1858T>G
NG_008412.1:g.6704A>C
NM_001318193.2:c.319A>C
NM_001318194.2:c.24+117A>C
NM_002528.7:c.319A>CMANE SELECT
NP_001305122.2:p.Thr107Pro
NP_002519.2:p.Thr107Pro
LRG_1366t1:c.319A>C
LRG_1366:g.6704A>C
LRG_1366p1:p.Thr107Pro
LRG_487:g.1858T>G
NC_000016.9:g.2096164T>G
NM_002528.5:c.343A>C
NM_002528.6:c.343A>C

Protein change:

T107P

Links:

dbSNP: rs1015524126

NCBI 1000 Genomes Browser:

rs1015524126

Molecular consequence:

NM_001318194.2:c.24+117A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001318193.2:c.319A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_002528.7:c.319A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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LOW QUALITY PROTEIN: kinesin-like protein KIF1C [Nomascus leucogenys]
LOW QUALITY PROTEIN: kinesin-like protein KIF1C [Nomascus leucogenys]
gi|1743177131|ref|XP_030655315.1|

Protein
Homo sapiens ABRA C-terminal like (ABRACL), mRNA
Homo sapiens ABRA C-terminal like (ABRACL), mRNA
gi|1519311527|ref|NM_021243.3|

Nucleotide
602584452F1 NIH_MGC_76 Homo sapiens cDNA clone IMAGE:4712125 5', mRNA sequence
602584452F1 NIH_MGC_76 Homo sapiens cDNA clone IMAGE:4712125 5', mRNA sequence
gi|13571338|gnl|dbEST|8275675|gb|BG 6.1|

Nucleotide
2005902[uid] (1)
Taxonomy
Lactobacillus jensenii strain UMB7766 NODE_23_length_15803_cov_41.498405, whole ...
Lactobacillus jensenii strain UMB7766 NODE_23_length_15803_cov_41.498405, whole genome shotgun sequence
gi|1828715850|ref|NZ_JAAUWC01000002 gnl|WGS:NZ_JAAUWC01|NODE_23_length_15803_cov_41.498405

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001212423	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 9, 2023)	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

SCV001212423

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 9, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001212423.5

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

Description

This sequence change replaces threonine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 115 of the NTHL1 protein (p.Thr115Pro). 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. ClinVar contains an entry for this variant (Variation ID: 845369). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Jun 23, 2024

ClinVar

Relating variation to medicine