ClinVar Genomic variation as it relates to human health
NM_000488.4(SERPINC1):c.218C>T (p.Pro73Leu)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000488.4(SERPINC1):c.218C>T (p.Pro73Leu)
Variation ID: 18011 Accession: VCV000018011.50
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1q25.1 1: 173914743 (GRCh38) [ NCBI UCSC ] 1: 173883881 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Dec 6, 2014 May 12, 2024 Sep 21, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000488.4:c.218C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000479.1:p.Pro73Leu missense NM_001365052.2:c.74C>T NP_001351981.1:p.Pro25Leu missense NM_001386302.1:c.218C>T NP_001373231.1:p.Pro73Leu missense NM_001386303.1:c.299C>T NP_001373232.1:p.Pro100Leu missense NM_001386304.1:c.218C>T NP_001373233.1:p.Pro73Leu missense NM_001386305.1:c.218C>T NP_001373234.1:p.Pro73Leu missense NM_001386306.1:c.218C>T NP_001373235.1:p.Pro73Leu missense NC_000001.11:g.173914743G>A NC_000001.10:g.173883881G>A NG_012462.1:g.7636C>T LRG_577:g.7636C>T LRG_577t1:c.218C>T LRG_577p1:p.Pro73Leu P01008:p.Pro73Leu - Protein change
- P73L, P25L, P100L
- Other names
- P41L
- NM_000488.3(SERPINC1):c.218C>T
- Canonical SPDI
- NC_000001.11:173914742:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00020 (A)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
1000 Genomes Project 30x 0.00016
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00043
Exome Aggregation Consortium (ExAC) 0.00072
The Genome Aggregation Database (gnomAD), exomes 0.00082
The Genome Aggregation Database (gnomAD) 0.00092
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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SERPINC1 | - | - |
GRCh38 GRCh37 |
359 | 416 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (12) |
reviewed by expert panel
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Sep 21, 2023 | RCV000019627.64 | |
Pathogenic/Likely pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Dec 8, 2021 | RCV001090508.30 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Sep 21, 2023)
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reviewed by expert panel
Method: curation
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Hereditary antithrombin deficiency
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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Clingen Thrombosis Variant Curation Expert Panel, ClinGen
FDA Recognized Database
Accession: SCV004037387.1 First in ClinVar: Oct 07, 2023 Last updated: Oct 07, 2023 |
Comment:
The c.218C>T (p.Pro73Leu) variant is reported at a POPMAX FAF of 0.0007473 in exomes in gnomAD v2.1.1 and at an FAF of 0.0006639 in genomes … (more)
The c.218C>T (p.Pro73Leu) variant is reported at a POPMAX FAF of 0.0007473 in exomes in gnomAD v2.1.1 and at an FAF of 0.0006639 in genomes in gnomAD v3.1.1 in the non-Finnish European population. The frequency does not meet the threshold for PM2_Supporting. At least 30 probands with AT deficiency and several others from internal laboratory data are reported with AT tests on 2 independent samples, meeting criteria for PS4_VeryStrong and PP4. There at least 17 meioses out of 35 families meeting PP1_Strong (PMID:28300866). This missense variant has a REVEL score of 0.658 (threshold >0.6), meeting criteria for PP3, and is within a heparin binding site, meeting PM1. In summary, this variant meets criteria to be classified as pathogenic. ACMG/AMP criteria applied, as specified by the Thrombosis Variant Curation Expert Panel for SERPINC1: PS4_VeryStrong, PP1_Strong, PM1, PP3, PP4. (less)
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Likely pathogenic
(Feb 01, 2019)
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criteria provided, single submitter
Method: research
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Hereditary antithrombin deficiency
Affected status: yes
Allele origin:
unknown
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NIHR Bioresource Rare Diseases, University of Cambridge
Study: ThromboGenomics
Accession: SCV000899323.1 First in ClinVar: Sep 29, 2019 Last updated: Sep 29, 2019 |
Observation 1:
Sex: female
Ethnicity/Population group: European
Observation 2:
Sex: female
Ethnicity/Population group: European
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Pathogenic
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Hereditary antithrombin deficiency
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000351487.3
First in ClinVar: Dec 06, 2016 Last updated: May 24, 2019 |
Comment:
The SERPINC1 c.218C>T (p.Pro73Leu) missense variant is well described in the literature. Across a selection of the available literature, the p.Pro73Leu variant, which is also … (more)
The SERPINC1 c.218C>T (p.Pro73Leu) missense variant is well described in the literature. Across a selection of the available literature, the p.Pro73Leu variant, which is also referred to as p.Pro41Leu, has been identified in a heterozygous state in four individuals diagnosed with antithrombin-III deficiency and with unspecified zygosity in 96 affected individuals (Chang et al. 1986; Molho-Sabatier et al. 1989; Puurunen et al. 2013; Feddersen et al. 2014). The p.Pro41Leu variant was absent from 106 controls, but is reported at a frequency of 0.00408 in the European (Finnish) population of the Exome Aggregation Consortium. Puurunen et al. (2013) suggest that the p.Pro73Leu variant is a founder variant in the Finnish population associated with type II hereditary antithrombin deficiency. The Pro73 residue is located at a heparin binding site. Bohdan et al. (2016) conducted a functional study to evaluate the effect of the p.Pro73Leu variant on binding affinity. The binding affinity between heparanase and antithrombin was greatly reduced in HEK-EBNA cells transfected with p.Pro73Leu variant plasmids compared to wildtype. Based on the collective evidence, the p.Pro73Leu variant is classified as pathogenic for antithrombin-III deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. (less)
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Pathogenic
(Sep 30, 2021)
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criteria provided, single submitter
Method: clinical testing
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Hereditary antithrombin deficiency
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001983481.1
First in ClinVar: Oct 30, 2021 Last updated: Oct 30, 2021 |
Comment:
Variant summary: SERPINC1 c.218C>T (p.Pro73Leu) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging … (more)
Variant summary: SERPINC1 c.218C>T (p.Pro73Leu) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00082 in 251456 control chromosomes, predominatly in the Finnish and non-Finnish European subpopulations with a frequency of 0.0044 and 0.00089 respectively. The variant, c.218C>T (aka. Pro41Leu or AT Basel), is well known variant in the literature and has been reported in numerous individuals affected with Antithrombin III Deficiency (e.g. Chang_1986 , Molho-Sabatier_1989, Puurunen_2013, Bereczky_2021), and is considered to be a founder variant in the Finnish population (Puurunen_2013). Several of these publications reported significantly reduced antithrombin activity in carriers. Publications also reported experimental evidence evaluating an impact on protein function, and demonstrated reduced heparin binding properties (Martinez-Martinez_2012, Bohdan_2016). Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014, and all laboratories classified the variant as pathogenic (n=3) / likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(Apr 22, 2022)
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criteria provided, single submitter
Method: clinical testing
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Hereditary antithrombin deficiency
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002810338.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Likely pathogenic
(Dec 08, 2021)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001820746.3
First in ClinVar: Sep 08, 2021 Last updated: Mar 04, 2023 |
Comment:
Published functional studies demonstrate defects in heparin binding properties (Martinez-Martinez, 2012; Bohdan et al., 2016); Reported previously as P41L or AT Basel using alternate nomenclature; … (more)
Published functional studies demonstrate defects in heparin binding properties (Martinez-Martinez, 2012; Bohdan et al., 2016); Reported previously as P41L or AT Basel using alternate nomenclature; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 24196373, 24956267, 26748602, 22498748, 25637381, 3080419, 28317092, 2794060, 23910795, 27322195, 24082793, 29902631, 28300866, 30721820, 25837307, 31589614, 33614741) (less)
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Likely pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Hereditary antithrombin deficiency
Affected status: yes
Allele origin:
germline
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ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology
Accession: SCV002515499.3
First in ClinVar: May 21, 2022 Last updated: Jul 22, 2023
Comment:
Submitted to GoldVariant by Kathleen Freson, Center for Molecular and Vascular Biology, Leuven, Belgium
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Observation 1:
Clinical Features:
thrombosis (present)
Observation 2:
Clinical Features:
thrombosis (present)
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Pathogenic
(Jan 24, 2024)
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criteria provided, single submitter
Method: clinical testing
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Hereditary antithrombin deficiency
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000756581.7
First in ClinVar: Sep 09, 2017 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 73 of the SERPINC1 protein (p.Pro73Leu). … (more)
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 73 of the SERPINC1 protein (p.Pro73Leu). This variant is present in population databases (rs121909551, gnomAD 0.4%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with type II antithrombin deficiency (PMID: 2794060, 3080419, 23910795, 24082793, 24956267, 26748602, 28317092). It is commonly reported in individuals of Finnish ancestry (PMID: 2794060, 3080419, 23910795, 24082793, 24956267, 26748602, 28317092). This variant is also known as Pro41Leu or AT Basel. ClinVar contains an entry for this variant (Variation ID: 18011). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SERPINC1 protein function. Experimental studies have shown that this missense change affects SERPINC1 function (PMID: 2794060, 3080419, 24082793, 27322195). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Sep 01, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001246102.21
First in ClinVar: May 12, 2020 Last updated: May 12, 2024 |
Number of individuals with the variant: 2
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Likely pathogenic
(Jul 23, 2021)
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criteria provided, single submitter
Method: clinical testing
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Not provided
Affected status: unknown
Allele origin:
germline
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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV002573725.1
First in ClinVar: Sep 24, 2022 Last updated: Sep 24, 2022 |
Comment:
PM1, PS3, PS4_Moderate
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Pathogenic
(Apr 12, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary antithrombin deficiency
Affected status: yes
Allele origin:
germline
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Clinical Genetics Laboratory, Region Ostergotland
Accession: SCV003925554.1
First in ClinVar: May 20, 2023 Last updated: May 20, 2023
Comment:
PMID:25741868 (PS4, PP3, PS3)
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Likely pathogenic
(Feb 21, 2022)
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criteria provided, single submitter
Method: clinical testing
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Hereditary antithrombin deficiency
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002019179.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Oct 30, 2023)
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no assertion criteria provided
Method: clinical testing
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Hereditary antithrombin deficiency
Affected status: yes
Allele origin:
germline
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Zotz-Klimas Genetics Lab, MVZ Zotz Klimas
Accession: SCV004099345.1
First in ClinVar: Nov 04, 2023 Last updated: Nov 04, 2023 |
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Uncertain significance
(Mar 01, 1992)
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Flagged submission
flagged submission
Method: literature only
Reason: Conflicts with expert reviewed submission without evidence to support different classification
Source: ClinGen
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RECLASSIFIED - VARIANT OF UNKNOWN SIGNIFICANCE
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000039925.4
First in ClinVar: Apr 04, 2013 Last updated: Sep 09, 2017 |
Comment on evidence:
This variant, formerly titled THROMBOPHILIA DUE TO ANTITHROMBIN III DEFICIENCY, has been reclassified because its contribution to the phenotype has not been confirmed. AT-III Clichy, … (more)
This variant, formerly titled THROMBOPHILIA DUE TO ANTITHROMBIN III DEFICIENCY, has been reclassified because its contribution to the phenotype has not been confirmed. AT-III Clichy, a substitution of leucine for proline-41, was described by Chang and Tran (1986), Aiach et al. (1987), and Molho-Sabatier et al. (1989). The variant has also been called AT-III Clichy-2, AT-III Basel, AT-III Franconville. Aiach et al. (1987) found the mutation in heterozygous state in a 24-year-old woman presenting with a thoracic outlet syndrome. Perry and Carrell (1989) described the same substitution in this heparin-binding mutation, which was caused by a CGT-to-CAT change in exon 2. Olds et al. (1990) noted that this mutation occurs within a CG dinucleotide, a recognized hotspot for single base mutations. In a woman referred for routine prepregnancy testing and in several members of her family, de Roux et al. (1990) found heterozygosity for the pro41-to-leu mutation. None had had thrombotic complications. Testing of the properties of the mutant AT-III suggested that proline-41 is more involved in the molecular changes induced by heparin than in the primary binding of the activator. (less)
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Likely benign
(Jun 01, 2014)
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Flagged submission
flagged submission
Method: research
Reason: Conflicts with expert reviewed submission without evidence to support different classification
Source: ClinGen
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Antithrombin deficiency
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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CSER _CC_NCGL, University of Washington
Study: ESP 6500 variant annotation
Accession: SCV000190626.1 First in ClinVar: Dec 06, 2014 Last updated: Dec 06, 2014
Comment:
Variants classified for the Actionable exomic incidental findings in 6503 participants: challenges of variant classification manuscript
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Flagged submissions do not contribute to the aggregate classification or review status for the variant. Learn more |
Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Molecular and clinical characterization of transient antithrombin deficiency: A new concept in congenital thrombophilia. | Bravo-Pérez C | American journal of hematology | 2022 | PMID: 34800304 |
Investigation of the Differences in Antithrombin to Heparin Binding among Antithrombin Budapest 3, Basel, and Padua Mutations by Biochemical and In Silico Methods. | Gindele R | Biomolecules | 2021 | PMID: 33917853 |
Age and Origin of the Founder Antithrombin Budapest 3 (p.Leu131Phe) Mutation; Its High Prevalence in the Roma Population and Its Association With Cardiovascular Diseases. | Bereczky Z | Frontiers in cardiovascular medicine | 2021 | PMID: 33614741 |
Diagnostic high-throughput sequencing of 2396 patients with bleeding, thrombotic, and platelet disorders. | Downes K | Blood | 2019 | PMID: 31064749 |
SERPINC1 variants causing hereditary antithrombin deficiency in a Danish population. | Kjaergaard AD | Thrombosis research | 2019 | PMID: 30721820 |
Clinical and laboratory characteristics of antithrombin deficiencies: A large cohort study from a single diagnostic center. | Gindele R | Thrombosis research | 2017 | PMID: 29153735 |
SERPINC1 gene mutations in antithrombin deficiency. | Mulder R | British journal of haematology | 2017 | PMID: 28317092 |
Thrombotic risk according to SERPINC1 genotype in a large cohort of subjects with antithrombin inherited deficiency. | Alhenc-Gelas M | Thrombosis and haemostasis | 2017 | PMID: 28300866 |
Heparanase Activates Antithrombin through the Binding to Its Heparin Binding Site. | Bohdan N | PloS one | 2016 | PMID: 27322195 |
Antithrombin heparin binding site deficiency: A challenging diagnosis of a not so benign thrombophilia. | Orlando C | Thrombosis research | 2015 | PMID: 25837307 |
Development of a novel, rapid assay for detection of heparin-binding defect antithrombin deficiencies: the heparin-antithrombin binding (HAB) ratio. | Moore GW | Thrombosis research | 2015 | PMID: 25466846 |
Discordant diagnoses obtained by different approaches in antithrombin mutation analysis. | Feddersen S | Clinical biochemistry | 2014 | PMID: 24956267 |
Impact of the type of SERPINC1 mutation and subtype of antithrombin deficiency on the thrombotic phenotype in hereditary antithrombin deficiency. | Luxembourg B | Thrombosis and haemostasis | 2014 | PMID: 24196373 |
Use of recombinant human antithrombin concentrate in pregnancy. | Kreuziger LM | International journal of women's health | 2013 | PMID: 24082793 |
Type II antithrombin deficiency caused by a founder mutation Pro73Leu in the Finnish population: clinical picture. | Puurunen M | Journal of thrombosis and haemostasis : JTH | 2013 | PMID: 23910795 |
Amelioration of the severity of heparin-binding antithrombin mutations by posttranslational mosaicism. | Martínez-Martínez I | Blood | 2012 | PMID: 22498748 |
Antithrombins Southport (Leu 99 to Val) and Vienna (Gln 118 to Pro): two novel antithrombin variants with abnormal heparin binding. | Chowdhury V | British journal of haematology | 1995 | PMID: 7734360 |
Antithrombin III Budapest: a single amino acid substitution (429Pro to Leu) in a region highly conserved in the serpin family. | Olds RJ | Blood | 1992 | PMID: 1536946 |
The incidence of dysfunctional antithrombin variants: four cases in 210 patients with thromboembolic disease. | Harper PL | British journal of haematology | 1991 | PMID: 2012760 |
Clinical and biochemical characterization of antithrombin III Franconville, a variant with Pro 41 Leu mutation. | de Roux N | British journal of haematology | 1990 | PMID: 2372510 |
Molecular characterization of antithrombin III (ATIII) variants using polymerase chain reaction. Identification of the ATIII Charleville as an Ala 384 Pro mutation. | Molho-Sabatier P | The Journal of clinical investigation | 1989 | PMID: 2794060 |
CpG dinucleotides are "hotspots" for mutation in the antithrombin III gene. Twelve variants identified using the polymerase chain reaction. | Perry DJ | Molecular biology & medicine | 1989 | PMID: 2615648 |
An abnormal antithrombin III (AT III) with low heparin affinity: AT III Clichy. | Aiach M | British journal of haematology | 1987 | PMID: 3663508 |
Antithrombin III Basel. Identification of a Pro-Leu substitution in a hereditary abnormal antithrombin with impaired heparin cofactor activity. | Chang JY | The Journal of biological chemistry | 1986 | PMID: 3080419 |
Purification and partial characterization of a hereditary abnormal antithrombin III fraction of a patient with recurrent thrombophlebitis. | Tran TH | Thrombosis and haemostasis | 1980 | PMID: 7455996 |
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/b7a99380-d40e-4611-81d1-d60401803a33 | - | - | - | - |
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Text-mined citations for rs121909551 ...
HelpRecord last updated May 27, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.