NM_000488.4(SERPINC1):c.771del (p.Leu256_Trp257insTer) AND Hereditary antithrombin deficiency

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 1, 2019
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:: RCV000852207.1

Allele description [Variation Report for NM_000488.4(SERPINC1):c.771del (p.Leu256_Trp257insTer)]

NM_000488.4(SERPINC1):c.771del (p.Leu256_Trp257insTer)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

1q25.1

Genomic location:

Preferred name:

NM_000488.4(SERPINC1):c.771del (p.Leu256_Trp257insTer)

HGVS:

NC_000001.11:g.173909935del
NG_012462.1:g.12445del
NM_000488.4:c.771delMANE SELECT
NM_001365052.2:c.627del
NM_001386302.1:c.894del
NM_001386303.1:c.852del
NM_001386304.1:c.750del
NM_001386305.1:c.763-49del
NM_001386306.1:c.555del
NP_000479.1:p.Leu256_Trp257insTer
NP_001351981.1:p.Leu208_Trp209insTer
NP_001373231.1:p.Leu297_Trp298insTer
NP_001373232.1:p.Leu283_Trp284insTer
NP_001373233.1:p.Leu249_Trp250insTer
NP_001373235.1:p.Leu184_Trp185insTer
LRG_577:g.12445del
NC_000001.10:g.173879073del
NM_000488.3:c.771delG

Links:

dbSNP: rs1572088853

NCBI 1000 Genomes Browser:

rs1572088853

Molecular consequence:

NM_001386305.1:c.763-49del - intron variant - [Sequence Ontology: SO:0001627]
NM_000488.4:c.771del - nonsense - [Sequence Ontology: SO:0001587]
NM_001365052.2:c.627del - nonsense - [Sequence Ontology: SO:0001587]
NM_001386302.1:c.894del - nonsense - [Sequence Ontology: SO:0001587]
NM_001386303.1:c.852del - nonsense - [Sequence Ontology: SO:0001587]
NM_001386304.1:c.750del - nonsense - [Sequence Ontology: SO:0001587]
NM_001386306.1:c.555del - 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

Recent activity

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Candidatus Kryptonium thompsonii strain JGI-5, whole genome shotgun sequence
Candidatus Kryptonium thompsonii strain JGI-5, whole genome shotgun sequence
gi|1129467480|ref|NZ_CZVS01000083.1

Nucleotide
BJ099936 NIBB Mochii normalized Xenopus early gastrula library Xenopus laevis cD...
BJ099936 NIBB Mochii normalized Xenopus early gastrula library Xenopus laevis cDNA clone XL155k02 3', mRNA sequence
gi|17602488|gnl|dbEST|10568259|dbj| 936.1|

Nucleotide
AGENCOURT_54841616 NICHD_XGC_Emb10 Xenopus laevis cDNA clone IMAGE:7982808 5', m...
AGENCOURT_54841616 NICHD_XGC_Emb10 Xenopus laevis cDNA clone IMAGE:7982808 5', mRNA sequence
gi|70901495|gnl|dbEST|30216161|gb|D 83.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000899912	NIHR Bioresource Rare Diseases, University of Cambridge - ThromboGenomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 1, 2019)	unknown	research	PubMed (2) [See all records that cite these PMIDs] 25741868, 31064749

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000899912

NIHR Bioresource Rare Diseases, University of Cambridge - ThromboGenomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 1, 2019)

unknown

research

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
European	unknown	yes	1	not provided	not provided	1	not provided	research

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Diagnostic high-throughput sequencing of 2396 patients with bleeding, thrombotic, and platelet disorders.

Downes K, Megy K, Duarte D, Vries M, Gebhart J, Hofer S, Shamardina O, Deevi SVV, Stephens J, Mapeta R, Tuna S, Al Hasso N, Besser MW, Cooper N, Daugherty L, Gleadall N, Greene D, Haimel M, Martin H, Papadia S, Revel-Vilk S, Sivapalaratnam S, et al.

Blood. 2019 Dec 5;134(23):2082-2091. doi: 10.1182/blood.2018891192.

PubMed [citation]

PMID:: 31064749
PMCID:: PMC6993014

Details of each submission

From NIHR Bioresource Rare Diseases, University of Cambridge - ThromboGenomics, SCV000899912.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	European	1	not provided	not provided	research	PubMed (2)

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

Last Updated: Oct 8, 2024

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