NM_080680.3(COL11A2):c.4789del (p.Asp1597fs) AND not provided

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 28, 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:: RCV003712220.1

Allele description

NM_080680.3(COL11A2):c.4789del (p.Asp1597fs)

Gene:

COL11A2:collagen type XI alpha 2 chain [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

6p21.32

Genomic location:

Preferred name:

NM_080680.3(COL11A2):c.4789del (p.Asp1597fs)

HGVS:

NC_000006.12:g.33164928del
NG_011589.1:g.32543del
NM_001424108.1:c.4609del
NM_001424109.1:c.3943del
NM_001424110.1:c.3763del
NM_001424111.1:c.3763del
NM_001424112.1:c.2743del
NM_080679.3:c.4468del
NM_080680.3:c.4789delMANE SELECT
NM_080681.3:c.4531del
NP_001411037.1:p.Asp1537fs
NP_001411038.1:p.Asp1315fs
NP_001411039.1:p.Asp1255fs
NP_001411040.1:p.Asp1255fs
NP_001411041.1:p.Asp915fs
NP_542410.2:p.Asp1490fs
NP_542411.2:p.Asp1597fs
NP_542412.2:p.Asp1511fs
NC_000006.11:g.33132703del
NC_000006.11:g.33132705del

Protein change:

D1255fs

Molecular consequence:

NM_001424108.1:c.4609del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001424109.1:c.3943del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001424110.1:c.3763del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001424111.1:c.3763del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001424112.1:c.2743del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_080679.3:c.4468del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_080680.3:c.4789del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_080681.3:c.4531del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV004475903	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 28, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10677296, 21204229, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004475903

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 28, 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

Autosomal recessive disorder otospondylomegaepiphyseal dysplasia is associated with loss-of-function mutations in the COL11A2 gene.

Melkoniemi M, Brunner HG, Manouvrier S, Hennekam R, Superti-Furga A, Kääriäinen H, Pauli RM, van Essen T, Warman ML, Bonaventure J, Miny P, Ala-Kokko L.

Am J Hum Genet. 2000 Feb;66(2):368-77.

PubMed [citation]

PMID:: 10677296
PMCID:: PMC1288089

A novel homozygous COL11A2 deletion causes a C-terminal protein truncation with incomplete mRNA decay in a Turkish patient.

Kayserili H, Wollnik B, Güven G, Emiroğlu MU, Başerer N, Uyguner ZO.

Am J Med Genet A. 2011 Jan;155A(1):180-5. doi: 10.1002/ajmg.a.33780.

PubMed [citation]

PMID:: 21204229

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004475903.1

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

Description

This sequence change creates a premature translational stop signal (p.Asp1597Metfs*17) in the COL11A2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COL11A2 are known to be pathogenic (PMID: 10677296, 21204229). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with COL11A2-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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