NM_000488.4(SERPINC1):c.1009C>T (p.Gln337Ter) AND Hereditary antithrombin deficiency

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 1, 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:: RCV003527187.1

Allele description

NM_000488.4(SERPINC1):c.1009C>T (p.Gln337Ter)

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.1009C>T (p.Gln337Ter)

HGVS:

NC_000001.11:g.173909696G>A
NG_012462.1:g.12683C>T
NM_000488.4:c.1009C>TMANE SELECT
NM_001365052.2:c.865C>T
NM_001386302.1:c.1132C>T
NM_001386303.1:c.1090C>T
NM_001386304.1:c.988C>T
NM_001386305.1:c.952C>T
NM_001386306.1:c.793C>T
NP_000479.1:p.Gln337Ter
NP_000479.1:p.Gln337Ter
NP_001351981.1:p.Gln289Ter
NP_001373231.1:p.Gln378Ter
NP_001373232.1:p.Gln364Ter
NP_001373233.1:p.Gln330Ter
NP_001373234.1:p.Gln318Ter
NP_001373235.1:p.Gln265Ter
LRG_577t1:c.1009C>T
LRG_577:g.12683C>T
LRG_577p1:p.Gln337Ter
NC_000001.10:g.173878834G>A
NM_000488.3:c.1009C>T

Protein change:

Q265*

Molecular consequence:

NM_000488.4:c.1009C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001365052.2:c.865C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001386302.1:c.1132C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001386303.1:c.1090C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001386304.1:c.988C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001386305.1:c.952C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001386306.1:c.793C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Hereditary antithrombin deficiency
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
SCV004293836	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 1, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24684277, 21264449, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004293836

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 1, 2023)

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

Clinical presentation and molecular basis of congenital antithrombin deficiency in children: a cohort study.

Kumar R, Chan AK, Dawson JE, Forman-Kay JD, Kahr WH, Williams S.

Br J Haematol. 2014 Jul;166(1):130-9. doi: 10.1111/bjh.12842. Epub 2014 Mar 29.

PubMed [citation]

PMID:: 24684277

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

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004293836.1

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

Description

For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with clinical features of antithrombin III deficiency (PMID: 24684277). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln337*) 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).

#	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: Feb 20, 2024

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