NM_080424.4(SP110):c.832A>G (p.Lys278Glu) AND Hepatic veno-occlusive disease-immunodeficiency syndrome

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 3, 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:: RCV003613814.1

Allele description

NM_080424.4(SP110):c.832A>G (p.Lys278Glu)

Genes:

SP110:SP110 nuclear body protein [Gene - OMIM - HGNC]
SP140:SP140 nuclear body protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q37.1

Genomic location:

Preferred name:

NM_080424.4(SP110):c.832A>G (p.Lys278Glu)

HGVS:

NC_000002.12:g.230208057T>C
NG_008295.1:g.17056A>G
NG_051286.1:g.10134T>C
NG_051286.2:g.26908T>C
NM_001185015.2:c.850A>G
NM_001378442.1:c.850A>G
NM_001378443.1:c.832A>G
NM_001378444.1:c.850A>G
NM_001378445.1:c.850A>G
NM_001378446.1:c.850A>G
NM_001378447.1:c.832A>G
NM_004509.5:c.832A>G
NM_004510.4:c.832A>G
NM_080424.4:c.832A>GMANE SELECT
NP_001171944.1:p.Lys284Glu
NP_001365371.1:p.Lys284Glu
NP_001365372.1:p.Lys278Glu
NP_001365373.1:p.Lys284Glu
NP_001365374.1:p.Lys284Glu
NP_001365375.1:p.Lys284Glu
NP_001365376.1:p.Lys278Glu
NP_004500.4:p.Lys278Glu
NP_004501.4:p.Lys278Glu
NP_536349.2:p.Lys278Glu
NP_536349.3:p.Lys278Glu
LRG_109t1:c.832A>G
LRG_109:g.17056A>G
LRG_109p1:p.Lys278Glu
NC_000002.11:g.231072772T>C
NM_080424.2:c.832A>G

Protein change:

K278E

Molecular consequence:

NM_001185015.2:c.850A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378442.1:c.850A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378443.1:c.832A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378444.1:c.850A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378445.1:c.850A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378446.1:c.850A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378447.1:c.832A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004509.5:c.832A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004510.4:c.832A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_080424.4:c.832A>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV004490308	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 3, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004490308

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 3, 2023)

germline

clinical testing

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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV004490308.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with SP110-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 278 of the SP110 protein (p.Lys278Glu).

#	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 28, 2024

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