NM_000128.4(F11):c.1613C>T (p.Pro538Leu) AND Hereditary factor XI deficiency disease

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: May 4, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000169580.4

Allele description [Variation Report for NM_000128.4(F11):c.1613C>T (p.Pro538Leu)]

NM_000128.4(F11):c.1613C>T (p.Pro538Leu)

Genes:

F11-AS1:F11 antisense RNA 1 [Gene - HGNC]
F11:coagulation factor XI [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q35.2

Genomic location:

Preferred name:

NM_000128.4(F11):c.1613C>T (p.Pro538Leu)

HGVS:

NC_000004.12:g.186287720C>T
NG_008051.1:g.26757C>T
NM_000128.4:c.1613C>TMANE SELECT
NP_000119.1:p.Pro538Leu
NP_000119.1:p.Pro538Leu
LRG_583t1:c.1613C>T
LRG_583:g.26757C>T
LRG_583p1:p.Pro538Leu
NC_000004.11:g.187208874C>T
NM_000128.3:c.1613C>T
P03951:p.Pro538Leu

Protein change:

P538L

Links:

UniProtKB: P03951#VAR_054903; dbSNP: rs139695003

NCBI 1000 Genomes Browser:

rs139695003

Molecular consequence:

NM_000128.4:c.1613C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary factor XI deficiency disease
Synonyms:: Plasma thromboplastin antecedent deficiency; PTA deficiency; Rosenthal syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012897; MeSH: D005173; MedGen: C0015523; Orphanet: 329; OMIM: 612416

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000221084	Counsyl	criteria provided, single submitter (Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))	Likely pathogenic (Jan 26, 2015)	unknown	literature only	PubMed (3) [See all records that cite these PMIDs] 17229051, 19652879, 15953011 Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015), Citation Link,
SCV000899536	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
SCV002519643	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Pathogenic (May 4, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000221084

Counsyl

criteria provided, single submitter

(Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))

Likely pathogenic
(Jan 26, 2015)

unknown

literature only

PubMed (3)
[See all records that cite these PMIDs]

Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015),

Citation Link,

SCV000899536

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]

SCV002519643

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2019)

Pathogenic
(May 4, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
European	unknown	yes	1	not provided	not provided	1	not provided	research

Citations

PubMed

A cross-reactive material positive variant of coagulation factor XI (FXIP520L) with a catalytic defect.

Gailani D, Schmidt A, Sun MF, Bolton-Maggs PH, Bajaj SP.

J Thromb Haemost. 2007 Apr;5(4):781-7. Epub 2007 Jan 9.

PubMed [citation]

PMID:: 17229051

Structural analysis of eight novel and 112 previously reported missense mutations in the interactive FXI mutation database reveals new insight on FXI deficiency.

Saunders RE, Shiltagh N, Gomez K, Mellars G, Cooper C, Perry DJ, Tuddenham EG, Perkins SJ.

Thromb Haemost. 2009 Aug;102(2):287-301. doi: 10.1160/TH09-01-0044.

PubMed [citation]

PMID:: 19652879

See all PubMed Citations (5)

Details of each submission

From Counsyl, SCV000221084.2

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

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

From NIHR Bioresource Rare Diseases, University of Cambridge - ThromboGenomics, SCV000899536.1

#	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

From Mendelics, SCV002519643.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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 30, 2024

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