NM_000506.5(F2):c.13C>T (p.Arg5Ter) AND Congenital prothrombin deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 14, 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:: RCV003627748.2

Allele description [Variation Report for NM_000506.5(F2):c.13C>T (p.Arg5Ter)]

NM_000506.5(F2):c.13C>T (p.Arg5Ter)

Gene:

F2:coagulation factor II, thrombin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p11.2

Genomic location:

Preferred name:

NM_000506.5(F2):c.13C>T (p.Arg5Ter)

HGVS:

NC_000011.10:g.46719248C>T
NG_008953.1:g.5056C>T
NM_000506.5:c.13C>TMANE SELECT
NP_000497.1:p.Arg5Ter
NP_000497.1:p.Arg5Ter
LRG_551t1:c.13C>T
LRG_551:g.5056C>T
LRG_551p1:p.Arg5Ter
NC_000011.9:g.46740798C>T
NM_000506.4:c.13C>T

Protein change:

R5*

Molecular consequence:

NM_000506.5:c.13C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Congenital prothrombin deficiency
Synonyms:: HYPOPROTHROMBINEMIA; Factor II deficiency; Hereditary factor II deficiency disease; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0013361; MedGen: C0272317; Orphanet: 325; OMIM: 613679

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MULTISPECIES: 30S ribosomal protein S21 [Bacteria]
MULTISPECIES: 30S ribosomal protein S21 [Bacteria]
gi|489244775|ref|WP_003152957.1|

Protein
MAPK cascade adaptor protein Ste4 [Schizosaccharomyces pombe]
MAPK cascade adaptor protein Ste4 [Schizosaccharomyces pombe]
gi|19114195|ref|NP_593283.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004401455	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 14, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23852823, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004401455

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 14, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Congenital prothrombin deficiency: an update.

Lancellotti S, Basso M, De Cristofaro R.

Semin Thromb Hemost. 2013 Sep;39(6):596-606. doi: 10.1055/s-0033-1348948. Epub 2013 Jul 12. Review.

PubMed [citation]

PMID:: 23852823

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004401455.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with F2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg5*) in the F2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in F2 are known to be pathogenic (PMID: 23852823).

#	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: Sep 29, 2024

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