NM_080424.4(SP110):c.1631dup (p.Gln545fs) AND Hepatic veno-occlusive disease-immunodeficiency syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 8, 2022
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:: RCV003106862.4

Allele description [Variation Report for NM_080424.4(SP110):c.1631dup (p.Gln545fs)]

NM_080424.4(SP110):c.1631dup (p.Gln545fs)

Gene:

SP110:SP110 nuclear body protein [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

2q37.1

Genomic location:

Preferred name:

NM_080424.4(SP110):c.1631dup (p.Gln545fs)

HGVS:

NC_000002.12:g.230172923dup
NG_008295.1:g.52193dup
NM_001378442.1:c.1649dup
NM_001378443.1:c.1631dup
NM_001378444.1:c.1649dup
NM_001378445.1:c.1649dup
NM_001378446.1:c.1649dup
NM_004509.5:c.1631dup
NM_080424.4:c.1631dupMANE SELECT
NP_001365371.1:p.Gln551fs
NP_001365372.1:p.Gln545fs
NP_001365373.1:p.Gln551fs
NP_001365374.1:p.Gln551fs
NP_001365375.1:p.Gln551fs
NP_004500.4:p.Gln545fs
NP_536349.3:p.Gln545fs
LRG_109:g.52193dup
NC_000002.11:g.231037634_231037635insC
NC_000002.11:g.231037639dup

Protein change:

Q545fs

Links:

dbSNP: rs2078486744

NCBI 1000 Genomes Browser:

rs2078486744

Molecular consequence:

NM_001378442.1:c.1649dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001378443.1:c.1631dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001378444.1:c.1649dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001378445.1:c.1649dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001378446.1:c.1649dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004509.5:c.1631dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_080424.4:c.1631dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Hepatic veno-occlusive disease-immunodeficiency syndrome
Synonyms:: Hepatic venoocclusive disease with immunodeficiency; Hepatic Veno-occlusive Disease with Immunodeficiency
Identifiers:: MONDO: MONDO:0009338; MedGen: C1856128; Orphanet: 79124; OMIM: 235550

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003782049	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 8, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 16648851, 22621957, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003782049

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 8, 2022)

germline

clinical testing

PubMed (3)
[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

Mutations in the gene encoding the PML nuclear body protein Sp110 are associated with immunodeficiency and hepatic veno-occlusive disease.

Roscioli T, Cliffe ST, Bloch DB, Bell CG, Mullan G, Taylor PJ, Sarris M, Wang J, Donald JA, Kirk EP, Ziegler JB, Salzer U, McDonald GB, Wong M, Lindeman R, Buckley MF.

Nat Genet. 2006 Jun;38(6):620-2. Epub 2006 Apr 30.

PubMed [citation]

PMID:: 16648851

Clinical, molecular, and cellular immunologic findings in patients with SP110-associated veno-occlusive disease with immunodeficiency syndrome.

Cliffe ST, Bloch DB, Suryani S, Kamsteeg EJ, Avery DT, Palendira U, Church JA, Wainstein BK, Trizzino A, Lefranc G, Akatcherian C, Megarbané A, Gilissen C, Moshous D, Reichenbach J, Misbah S, Salzer U, Abinun M, Ong PY, Stepensky P, Ruga E, Ziegler JB, et al.

J Allergy Clin Immunol. 2012 Sep;130(3):735-742.e6. doi: 10.1016/j.jaci.2012.02.054. Epub 2012 May 21.

PubMed [citation]

PMID:: 22621957

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003782049.3

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

Description

This variant has not been reported in the literature in individuals affected with SP110-related conditions. For these reasons, this variant has been classified as Pathogenic. This sequence change creates a premature translational stop signal (p.Gln545Thrfs*14) in the SP110 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SP110 are known to be pathogenic (PMID: 16648851, 22621957). This variant is not present in population databases (gnomAD no frequency).

#	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: Feb 20, 2024

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