NM_000488.4(SERPINC1):c.1256C>T (p.Ala419Val) AND Hereditary antithrombin deficiency

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Nov 4, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000019654.38

Allele description [Variation Report for NM_000488.4(SERPINC1):c.1256C>T (p.Ala419Val)]

NM_000488.4(SERPINC1):c.1256C>T (p.Ala419Val)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

1q25.1

Genomic location:

Preferred name:

NM_000488.4(SERPINC1):c.1256C>T (p.Ala419Val)

Other names:

A387V

HGVS:

NC_000001.11:g.173904028G>A
NG_012462.1:g.18351C>T
NM_000488.4:c.1256C>TMANE SELECT
NM_001365052.2:c.1112C>T
NM_001386302.1:c.1379C>T
NM_001386303.1:c.1337C>T
NM_001386304.1:c.1235C>T
NM_001386305.1:c.1199C>T
NM_001386306.1:c.1040C>T
NP_000479.1:p.Ala419Val
NP_000479.1:p.Ala419Val
NP_001351981.1:p.Ala371Val
NP_001373231.1:p.Ala460Val
NP_001373232.1:p.Ala446Val
NP_001373233.1:p.Ala412Val
NP_001373234.1:p.Ala400Val
NP_001373235.1:p.Ala347Val
LRG_577t1:c.1256C>T
LRG_577:g.18351C>T
LRG_577p1:p.Ala419Val
NC_000001.10:g.173873166G>A
NM_000488.3:c.1256C>T
P01008:p.Ala419Val

Protein change:

A347V; ALA387VAL

Links:

UniProtKB: P01008#VAR_007072; OMIM: 107300.0042; dbSNP: rs121909568

NCBI 1000 Genomes Browser:

rs121909568

Molecular consequence:

NM_000488.4:c.1256C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001365052.2:c.1112C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001386302.1:c.1379C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001386303.1:c.1337C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001386304.1:c.1235C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001386305.1:c.1199C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001386306.1:c.1040C>T - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

Clear Turn Off Turn On

BJ030411 NIBB Mochii normalized Xenopus neurula library Xenopus laevis cDNA clon...
BJ030411 NIBB Mochii normalized Xenopus neurula library Xenopus laevis cDNA clone XL004b05 5', mRNA sequence
gi|17374073|gnl|dbEST|10469310|dbj| 411.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000039952	OMIM	no assertion criteria provided	Pathogenic (Dec 1, 1992)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000190627	CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation	criteria provided, single submitter (Amendola et al. (Genome Res. 2015))	Uncertain significance (Jun 1, 2014)	germline	research	PubMed (1) [See all records that cite this PMID]
SCV002800940	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 4, 2021)	unknown	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

SCV000039952

OMIM

no assertion criteria provided

Pathogenic
(Dec 1, 1992)

germline

literature only

PubMed (1)
[See all records that cite this PMID]

SCV000190627

CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation

criteria provided, single submitter

(Amendola et al. (Genome Res. 2015))

Uncertain significance
(Jun 1, 2014)

germline

research

PubMed (1)
[See all records that cite this PMID]

SCV002800940

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 4, 2021)

unknown

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	research
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A novel missense mutation in the antithrombin III gene (Ala387-->Val) causing recurrent venous thrombosis.

White D, Abraham G, Carter C, Kakkar VV, Cooper DN.

Hum Genet. 1992 Dec;90(4):472-3. No abstract available.

PubMed [citation]

PMID:: 1483709

Actionable exomic incidental findings in 6503 participants: challenges of variant classification.

Amendola LM, Dorschner MO, Robertson PD, Salama JS, Hart R, Shirts BH, Murray ML, Tokita MJ, Gallego CJ, Kim DS, Bennett JT, Crosslin DR, Ranchalis J, Jones KL, Rosenthal EA, Jarvik ER, Itsara A, Turner EH, Herman DS, Schleit J, Burt A, Jamal SM, et al.

Genome Res. 2015 Mar;25(3):305-15. doi: 10.1101/gr.183483.114. Epub 2015 Jan 30.

PubMed [citation]

PMID:: 25637381
PMCID:: PMC4352885

See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000039952.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a patient with recurrent venous thrombosis and an AT-III activity/antigen level consistent with type I AT-III deficiency (613118), White et al. (1992) identified heterozygosity for a C-T transition in the AT3 gene, resulting in an ala387-to-val substitution near the reactive site.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation, SCV000190627.2

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

Description

Low GERP score may suggest that this variant may belong in a lower pathogenicity class

#	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

From Fulgent Genetics, Fulgent Genetics, SCV002800940.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

ClinVar

Relating variation to medicine