NM_000488.4(SERPINC1):c.1016G>A (p.Trp339Ter) AND Hereditary antithrombin deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 7, 2021
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:: RCV001857426.4

Allele description [Variation Report for NM_000488.4(SERPINC1):c.1016G>A (p.Trp339Ter)]

NM_000488.4(SERPINC1):c.1016G>A (p.Trp339Ter)

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.1016G>A (p.Trp339Ter)

HGVS:

NC_000001.11:g.173909689C>T
NG_012462.1:g.12690G>A
NM_000488.4:c.1016G>AMANE SELECT
NM_001365052.2:c.872G>A
NM_001386302.1:c.1139G>A
NM_001386303.1:c.1097G>A
NM_001386304.1:c.995G>A
NM_001386305.1:c.959G>A
NM_001386306.1:c.800G>A
NP_000479.1:p.Trp339Ter
NP_000479.1:p.Trp339Ter
NP_001351981.1:p.Trp291Ter
NP_001373231.1:p.Trp380Ter
NP_001373232.1:p.Trp366Ter
NP_001373233.1:p.Trp332Ter
NP_001373234.1:p.Trp320Ter
NP_001373235.1:p.Trp267Ter
LRG_577t1:c.1016G>A
LRG_577:g.12690G>A
LRG_577p1:p.Trp339Ter
NC_000001.10:g.173878827C>T
NM_000488.3:c.1016G>A

Protein change:

W267*

Links:

dbSNP: rs483352856

NCBI 1000 Genomes Browser:

rs483352856

Molecular consequence:

NM_000488.4:c.1016G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001365052.2:c.872G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001386302.1:c.1139G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001386303.1:c.1097G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001386304.1:c.995G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001386305.1:c.959G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001386306.1:c.800G>A - nonsense - [Sequence Ontology: SO:0001587]

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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Mus musculus chromosome 15, clone RP23-82J20, complete sequence
Mus musculus chromosome 15, clone RP23-82J20, complete sequence
gi|67972625|gnl|WIBR|L14787|gb|AC14 14|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002182585	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 7, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 21264449, 23932013, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002182585

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 7, 2021)

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

Molecular basis of antithrombin deficiency.

Luxembourg B, Delev D, Geisen C, Spannagl M, Krause M, Miesbach W, Heller C, Bergmann F, Schmeink U, Grossmann R, Lindhoff-Last E, Seifried E, Oldenburg J, Pavlova A.

Thromb Haemost. 2011 Apr;105(4):635-46. doi: 10.1160/TH10-08-0538. Epub 2011 Jan 25.

PubMed [citation]

PMID:: 21264449

Molecular basis and thrombotic manifestations of antithrombin deficiency in 15 unrelated Chinese patients.

Ding Q, Wang M, Xu G, Ye X, Xi X, Yu T, Wang X, Wang H.

Thromb Res. 2013 Sep;132(3):367-73. doi: 10.1016/j.thromres.2013.07.013. Epub 2013 Aug 8.

PubMed [citation]

PMID:: 23932013

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002182585.3

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

Description

This sequence change creates a premature translational stop signal (p.Trp339*) in the SERPINC1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SERPINC1 are known to be pathogenic (PMID: 21264449). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 100923). This premature translational stop signal has been observed in individual(s) with antithrombin deficiency (PMID: 23932013). This variant is not present in population databases (ExAC no frequency).

#	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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