NM_000133.4(F9):c.-17A>G AND multiple conditions

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

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 30, 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:: RCV003764554.1

Allele description

NM_000133.4(F9):c.-17A>G

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.-17A>G

Other names:

F9, +13A-G

HGVS:

NC_000023.11:g.139530748A>G
NG_007994.1:g.5013A>G
NM_000133.4:c.-17A>GMANE SELECT
NM_001313913.2:c.-17A>G
LRG_556:g.5013A>G
NC_000023.10:g.138612907A>G

Nucleotide change:

+13A-G

Links:

OMIM: 300746.0090; dbSNP: rs1927322926

NCBI 1000 Genomes Browser:

rs1927322926

Molecular consequence:

NM_000133.4:c.-17A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001313913.2:c.-17A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

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

Recent activity

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long-chain fatty acid-CoA ligase FAA1 [Saccharomyces cerevisiae S288C]
long-chain fatty acid-CoA ligase FAA1 [Saccharomyces cerevisiae S288C]
gi|398366229|ref|NP_014962.3|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004571521	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Jan 30, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 31395865, 2917196, 17014892, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004571521

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Jan 30, 2023)

germline

clinical testing

PubMed (4)
[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

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution.

Kircher M, Xiong C, Martin B, Schubach M, Inoue F, Bell RJA, Costello JF, Shendure J, Ahituv N.

Nat Commun. 2019 Aug 8;10(1):3583. doi: 10.1038/s41467-019-11526-w.

PubMed [citation]

PMID:: 31395865
PMCID:: PMC6687891

Two novel point mutations correlate with an altered developmental expression of blood coagulation factor IX (hemophilia B Leyden phenotype).

Reitsma PH, Mandalaki T, Kasper CK, Bertina RM, Briët E.

Blood. 1989 Feb 15;73(3):743-6.

PubMed [citation]

PMID:: 2917196

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV004571521.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Studies have shown that this variant does not significantly alter or has an unclear effect on F9 gene expression (PMID: 31395865). ClinVar contains an entry for this variant (Variation ID: 10646). This variant is also known as A13G. This variant has been observed in individuals with hemophilia B (PMID: 2917196, 17014892). This variant is not present in population databases (gnomAD no frequency). This variant occurs in a non-coding region of the F9 gene. It does not change the encoded amino acid sequence of the F9 protein.

#	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: Mar 5, 2024

ClinVar

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