NM_002936.6(RNASEH1):c.641C>T (p.Thr214Met) AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 13, 2022
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:: RCV002605903.1

Allele description

NM_002936.6(RNASEH1):c.641C>T (p.Thr214Met)

Gene:

RNASEH1:ribonuclease H1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p25.3

Genomic location:

Preferred name:

NM_002936.6(RNASEH1):c.641C>T (p.Thr214Met)

HGVS:

NC_000002.12:g.3548648G>A
NG_051310.1:g.14724C>T
NM_001286834.3:c.563C>T
NM_001286837.3:c.290C>T
NM_001378271.1:c.641C>T
NM_001378272.1:c.638C>T
NM_001378273.1:c.626C>T
NM_002936.6:c.641C>TMANE SELECT
NP_001273763.1:p.Thr188Met
NP_001273766.1:p.Thr97Met
NP_001365200.1:p.Thr214Met
NP_001365201.1:p.Thr213Met
NP_001365202.1:p.Thr209Met
NP_002927.2:p.Thr214Met
LRG_1090t1:c.641C>T
LRG_1090:g.14724C>T
LRG_1090p1:p.Thr214Met
NC_000002.11:g.3596238G>A
NR_148532.2:n.714C>T
NR_148533.2:n.710C>T
NR_148534.2:n.714C>T
NR_165465.1:n.598C>T
NR_165466.1:n.683C>T
NR_165467.1:n.883C>T
NR_165468.1:n.686C>T

Protein change:

T188M

Molecular consequence:

NM_001286834.3:c.563C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001286837.3:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001378271.1:c.641C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001378272.1:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001378273.1:c.626C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002936.6:c.641C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_148532.2:n.714C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148533.2:n.710C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148534.2:n.714C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_165465.1:n.598C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_165466.1:n.683C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_165467.1:n.883C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_165468.1:n.686C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Psalidodon brachypterygium voucher UFRGS21849-TEC6844 NADH dehydrogenase subunit...
Psalidodon brachypterygium voucher UFRGS21849-TEC6844 NADH dehydrogenase subunit 2 gene, partial cds; mitochondrial
gi|1818799377|gb|MN020434.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003497111	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 13, 2022)	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

SCV003497111

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 13, 2022)

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, SCV003497111.1

#	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 methionine, which is neutral and non-polar, at codon 214 of the RNASEH1 protein (p.Thr214Met). This variant is present in population databases (rs187577328, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with RNASEH1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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: Mar 26, 2023

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