NC_000001.11:g.173917430G>C AND Hereditary antithrombin deficiency

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Oct 20, 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:: RCV003527194.2

Allele description [Variation Report for NC_000001.11:g.173917430G>C]

NC_000001.11:g.173917430G>C

Gene:

SERPINC1:serpin family C member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q25.1

Genomic location:

Preferred name:

NC_000001.11:g.173917430G>C

HGVS:

NC_000001.11:g.173917430G>C
NG_012462.1:g.4949C>G
LRG_577:g.4949C>G
NC_000001.10:g.173886568G>C

Condition(s)

Name:: Hereditary antithrombin deficiency (AT3D)
Synonyms:: Antithrombin III deficiency; Thrombophilia due to antithrombin III deficiency; Reduced antithrombin III activity; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0013144; MedGen: C0272375; OMIM: 613118; Human Phenotype Ontology: HP:0001976

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004293844	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Oct 20, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22234719, 27003919, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004293844

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Oct 20, 2022)

germline

clinical testing

PubMed (3)
[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

Regulatory regions of SERPINC1 gene: identification of the first mutation associated with antithrombin deficiency.

de la Morena-Barrio ME, Antón AI, Martínez-Martínez I, Padilla J, Miñano A, Navarro-Fernández J, Águila S, López MF, Fontcuberta J, Vicente V, Corral J.

Thromb Haemost. 2012 Mar;107(3):430-7. doi: 10.1160/TH11-10-0701. Epub 2012 Jan 11.

PubMed [citation]

PMID:: 22234719

Identification of Regulatory Mutations in SERPINC1 Affecting Vitamin D Response Elements Associated with Antithrombin Deficiency.

Toderici M, de la Morena-Barrio ME, Padilla J, Miñano A, Antón AI, Iniesta JA, Herranz MT, Fernández N, Vicente V, Corral J.

PLoS One. 2016;11(3):e0152159. doi: 10.1371/journal.pone.0152159. Erratum in: PLoS One. 2016 Jul 21;11(7):e0159987. doi: 10.1371/journal.pone.0159987.

PubMed [citation]

PMID:: 27003919
PMCID:: PMC4803246

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004293844.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Studies have shown that this variant alters SERPINC1 gene expression (PMID: 22234719). This variant is also known as g.2143C>G or c.1-171C>G. This variant has been observed in individual(s) with antithrombin III deficiency (PMID: 22234719, 27003919). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This variant occurs in a non-coding region of the SERPINC1 gene. It does not change the encoded amino acid sequence of the SERPINC1 protein.

#	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 8, 2024

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