NM_080424.4(SP110):c.3G>A (p.Met1Ile) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 17, 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:: RCV003155808.1

Allele description [Variation Report for NM_080424.4(SP110):c.3G>A (p.Met1Ile)]

NM_080424.4(SP110):c.3G>A (p.Met1Ile)

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.3G>A (p.Met1Ile)

HGVS:

NC_000002.12:g.230216925C>T
NG_008295.1:g.8188G>A
NG_051286.1:g.19002C>T
NG_051286.2:g.35776C>T
NM_001185015.2:c.21G>A
NM_001378442.1:c.21G>A
NM_001378443.1:c.3G>A
NM_001378444.1:c.21G>A
NM_001378445.1:c.21G>A
NM_001378446.1:c.21G>A
NM_001378447.1:c.3G>A
NM_004509.3:c.3G>A
NM_004509.5:c.3G>A
NM_004510.4:c.3G>A
NM_080424.4:c.3G>AMANE SELECT
NP_001171944.1:p.Met7Ile
NP_001365371.1:p.Met7Ile
NP_001365372.1:p.Met1Ile
NP_001365373.1:p.Met7Ile
NP_001365374.1:p.Met7Ile
NP_001365375.1:p.Met7Ile
NP_001365376.1:p.Met1Ile
NP_004500.4:p.Met1Ile
NP_004501.4:p.Met1Ile
NP_536349.2:p.Met1Ile
NP_536349.3:p.Met1Ile
LRG_109t1:c.3G>A
LRG_109:g.8188G>A
LRG_109p1:p.Met1Ile
NC_000002.11:g.231081640C>T
NM_080424.2:c.3G>A

Protein change:

M1I

Molecular consequence:

NM_001378443.1:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001378447.1:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_004509.5:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_004510.4:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_080424.4:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001185015.2:c.21G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378442.1:c.21G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378443.1:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378444.1:c.21G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378445.1:c.21G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378446.1:c.21G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378447.1:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004509.5:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004510.4:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_080424.4:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003844909	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Feb 17, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003844909

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Feb 17, 2023)

germline

clinical testing

Citation Link

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003844909.2

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

Description

Variant summary: SP110 c.3G>A (p.Met1Ile) alters the initiation codon and is predicted to result in truncation of the encoded protein due to translation initiation at a downstream codon. The variant was absent in 249750 control chromosomes. An alternative downstream in-frame start codon (Met3) is located in the encoded protein. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.3G>A in individuals affected with Hepatic Venoocclusive Disease With Immunodeficiency and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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: Sep 3, 2023

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