NM_000063.6(C2):c.630T>A (p.Tyr210Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 26, 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:: RCV003710278.1

Allele description [Variation Report for NM_000063.6(C2):c.630T>A (p.Tyr210Ter)]

NM_000063.6(C2):c.630T>A (p.Tyr210Ter)

Gene:

C2:complement C2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.33

Genomic location:

Preferred name:

NM_000063.6(C2):c.630T>A (p.Tyr210Ter)

HGVS:

NC_000006.12:g.31933880T>A
NG_011730.1:g.11392T>A
NM_000063.6:c.630T>AMANE SELECT
NM_001145903.3:c.234T>A
NM_001178063.3:c.261T>A
NM_001282457.2:c.111+97T>A
NM_001282458.2:c.543T>A
NM_001282459.2:c.630T>A
NP_000054.2:p.Tyr210Ter
NP_000054.2:p.Tyr210Ter
NP_001139375.1:p.Tyr78Ter
NP_001171534.1:p.Tyr87Ter
NP_001269387.1:p.Tyr181Ter
NP_001269388.1:p.Tyr210Ter
LRG_26t1:c.630T>A
LRG_26:g.11392T>A
LRG_26p1:p.Tyr210Ter
NC_000006.11:g.31901657T>A
NM_000063.4:c.630T>A

Protein change:

Y181*

Molecular consequence:

NM_001282457.2:c.111+97T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000063.6:c.630T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001145903.3:c.234T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001178063.3:c.261T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001282458.2:c.543T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001282459.2:c.630T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004478457	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 26, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 1577763, 9616367, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004478457

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 26, 2023)

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

Type I human complement C2 deficiency. A 28-base pair gene deletion causes skipping of exon 6 during RNA splicing.

Johnson CA, Densen P, Hurford RK Jr, Colten HR, Wetsel RA.

J Biol Chem. 1992 May 5;267(13):9347-53. Erratum in: J Biol Chem. 1993 Jan 25;268(3):2268..

PubMed [citation]

PMID:: 1577763

Molecular heterogeneity in deficiency of complement protein C2 type I.

Wang X, Circolo A, Lokki ML, Shackelford PG, Wetsel RA, Colten HR.

Immunology. 1998 Feb;93(2):184-91.

PubMed [citation]

PMID:: 9616367
PMCID:: PMC1364177

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004478457.1

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

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr210*) in the C2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in C2 are known to be pathogenic (PMID: 1577763, 9616367). This variant has not been reported in the literature in individuals affected with C2-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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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