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NM_000133.4(F9):c.88+2T>C AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 9, 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:
RCV001925914.3

Allele description

NM_000133.4(F9):c.88+2T>C

Gene:
F9:coagulation factor IX [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq27.1
Genomic location:
Preferred name:
NM_000133.4(F9):c.88+2T>C
HGVS:
  • NC_000023.11:g.139530854T>C
  • NG_007994.1:g.5119T>C
  • NM_000133.4:c.88+2T>CMANE SELECT
  • NM_001313913.2:c.88+2T>C
  • LRG_556:g.5119T>C
  • NC_000023.10:g.138613013T>C
Links:
dbSNP: rs2148353009
NCBI 1000 Genomes Browser:
rs2148353009
Molecular consequence:
  • NM_000133.4:c.88+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001313913.2:c.88+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Hereditary factor IX deficiency disease (HEMB)
Synonyms:
F9 DEFICIENCY; PLASMA THROMBOPLASTIN COMPONENT DEFICIENCY; Hemophilia B; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010604; MeSH: D002836; MedGen: C0008533; Orphanet: 98879; OMIM: 306900
Name:
Thrombophilia, X-linked, due to factor 9 defect
Synonyms:
Thrombophilia, X-linked, due to factor IX defect
Identifiers:
MONDO: MONDO:0010432; MedGen: C2749016; OMIM: 300807

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002180068Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 9, 2021) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Reported in vivo splice-site mutations in the factor IX gene: severity of splicing defects and a hypothesis for predicting deleterious splice donor mutations.

Ketterling RP, Drost JB, Scaringe WA, Liao DZ, Liu JZ, Kasper CK, Sommer SS.

Hum Mutat. 1999;13(3):221-31.

PubMed [citation]
PMID:
10090477

Identification of twenty-one new mutations in the factor IX gene by SSCP analysis.

Montejo JM, Magallón M, Tizzano E, Solera J.

Hum Mutat. 1999;13(2):160-5.

PubMed [citation]
PMID:
10094553
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV002180068.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant is also known as donor splice 119T>C. Disruption of this splice site has been observed in individuals with hemophilia B (PMID: 10090477, 10094553). This variant is not present in population databases (ExAC no frequency). This sequence change affects a donor splice site in intron 1 of the F9 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in F9 are known to be pathogenic (PMID: 20301668).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024