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NM_003764.4(STX11):c.173T>C (p.Leu58Pro) AND Familial hemophagocytic lymphohistiocytosis 4

Germline classification:
Pathogenic (4 submissions)
Last evaluated:
Mar 25, 2024
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:
RCV000083252.11

Allele description [Variation Report for NM_003764.4(STX11):c.173T>C (p.Leu58Pro)]

NM_003764.4(STX11):c.173T>C (p.Leu58Pro)

Gene:
STX11:syntaxin 11 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q24.2
Genomic location:
Preferred name:
NM_003764.4(STX11):c.173T>C (p.Leu58Pro)
HGVS:
  • NC_000006.12:g.144186800T>C
  • NG_007613.1:g.41284T>C
  • NM_003764.4:c.173T>CMANE SELECT
  • NP_003755.2:p.Leu58Pro
  • LRG_113t1:c.173T>C
  • LRG_113:g.41284T>C
  • NC_000006.11:g.144507937T>C
  • NM_003764.3:c.173T>C
Protein change:
L58P; LEU58PRO
Links:
OMIM: 605014.0004; dbSNP: rs431905512
NCBI 1000 Genomes Browser:
rs431905512
Molecular consequence:
  • NM_003764.4:c.173T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Familial hemophagocytic lymphohistiocytosis 4 (FHL4)
Identifiers:
MONDO: MONDO:0011336; MedGen: C1863728; Orphanet: 540; OMIM: 603552

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000115331OMIM
no assertion criteria provided
Pathogenic
(Jan 14, 2014)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV001133261Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City
no assertion criteria provided
Uncertain significance
(Sep 26, 2019)
germlineclinical testing

SCV001577802Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Nov 18, 2023)
germlineclinical testing

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

SCV004806140Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 25, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Cerebellar swelling due to familial hemophagocytic lymphohistiocytosis: An unusual presentation.

Khan SG, Binmahfoodh M, Alali M, Bayoumy M, Al-Said Y, Kayyali HR.

Eur J Paediatr Neurol. 2015 Sep;19(5):603-6. doi: 10.1016/j.ejpn.2015.04.009. Epub 2015 May 14.

PubMed [citation]
PMID:
26004995

An N-Terminal Missense Mutation in STX11 Causative of FHL4 Abrogates Syntaxin-11 Binding to Munc18-2.

Müller ML, Chiang SC, Meeths M, Tesi B, Entesarian M, Nilsson D, Wood SM, Nordenskjöld M, Henter JI, Naqvi A, Bryceson YT.

Front Immunol. 2014 Jan 14;4:515. doi: 10.3389/fimmu.2013.00515.

PubMed [citation]
PMID:
24459464
PMCID:
PMC3890652
See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000115331.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 3 unrelated Pakistani children with familial hemophagocytic lymphohistiocytosis (FHL4; 603552), each born of consanguineous parents, Muller et al. (2014) identified a homozygous c.173T-C transition in the STX11 gene, resulting in a leu58-to-pro (L58P) substitution in the first alpha-helix of the conserved N-terminal Habc domain. All of the parents were unaffected and heterozygous for the mutation. Peripheral blood cells, including NK cells, from 1 of the patients showed significantly decreased STX11 protein levels compared to controls. In vitro functional expression studies in HEK293 cells showed that the mutant L58P protein was expressed, but did not bind to STXBP2 (601717). In contrast, the C-terminal Q268X mutant protein (605014.0003) did not show impaired binding to STXBP2. Muller et al. (2014) suggested that the impaired binding to STXBP2 may have led to degradation of the mutant L58P STX11 protein. The patients presented in infancy or early childhood with clinical and laboratory evidence of a hyperinflammatory state. Resting patient NK cells showed defective lytic activity and impaired degranulation. One of the patients also carried a heterozygous P271S variant in the UNC13D gene (608897) (frequency of 0.001 among Caucasians) and a homozygous R928C variant in the UNC13D gene (frequency of 0.01 among Caucasians); this patient had the earliest onset, at age 2 months. Two of the patients died in childhood, and the third was lost to follow-up.

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

From Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City, SCV001133261.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001577802.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 58 of the STX11 protein (p.Leu58Pro). This variant is present in population databases (rs431905512, gnomAD 0.007%). This missense change has been observed in individuals with hemophagocytic lymphohistiocytosis (PMID: 24459464, 26004995; Invitae). ClinVar contains an entry for this variant (Variation ID: 97001). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt STX11 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects STX11 function (PMID: 24459464). For these reasons, this variant has been classified as Pathogenic.

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

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004806140.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 6, 2024