NM_001844.4(COL2A1):c.3138delT (p.Gly1047Alafs) AND Stickler syndrome type 1

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

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Oct 28, 2015
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:: RCV000018909.29

Allele description

NM_001844.4(COL2A1):c.3138delT (p.Gly1047Alafs)

Gene:

COL2A1:collagen type II alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q13.11

Genomic location:

Preferred name:

NM_001844.4(COL2A1):c.3138delT (p.Gly1047Alafs)

HGVS:

NC_000012.12:g.47977627delA
NM_001844.4:c.3138delT
NM_033150.2:c.2931delT
NP_001835.3:p.Gly1047Alafs
NP_149162.2:p.Gly978Alafs
NC_000012.11:g.48371410delA

Protein change:

P846*; PRO846TER

Links:

OMIM: 120140.0015; dbSNP: rs121912873

NCBI 1000 Genomes Browser:

rs121912873

Molecular consequence:

NM_001844.4:c.3138delT - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Stickler syndrome type 1 (STL1)
Identifiers:: MedGen: C2020284; Orphanet: 828; OMIM: 108300

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000039193	OMIM	no assertion criteria provided	Pathogenic (Jul 1, 1993)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000336451	EGL Genetic Diagnostics,Eurofins Clinical Diagnostics	criteria provided, single submitter (EGL Classification Definitions)	Pathogenic (Oct 28, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000039193

OMIM

no assertion criteria provided

Pathogenic
(Jul 1, 1993)

germline

literature only

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

SCV000336451

EGL Genetic Diagnostics,Eurofins Clinical Diagnostics

criteria provided, single submitter

(EGL Classification Definitions)

Pathogenic
(Oct 28, 2015)

germline

clinical testing

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

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A fourth example suggests that premature termination codons in the COL2A1 gene are a common cause of the Stickler syndrome: analysis of the COL2A1 gene by denaturing gradient gel electrophoresis.

Ritvaniemi P, Hyland J, Ignatius J, Kivirikko KI, Prockop DJ, Ala-Kokko L.

Genomics. 1993 Jul;17(1):218-21.

PubMed [citation]

PMID:: 8406454

Effect of ivacaftor on CFTR forms with missense mutations associated with defects in protein processing or function.

Van Goor F, Yu H, Burton B, Hoffman BJ.

J Cyst Fibros. 2014 Jan;13(1):29-36. doi: 10.1016/j.jcf.2013.06.008. Epub 2013 Jul 23.

PubMed [citation]

PMID:: 23891399

Details of each submission

From OMIM, SCV000039193.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a family with Stickler syndrome (STL1; 108300) in members of 4 successive generations, Ritvaniemi et al. (1993) found a deletion of a T in the third base position of the codon CCT for proline at position 846 of the collagen II alpha-1 chain. The deletion of the T shifted the reading frame and generated premature termination. Ritvaniemi et al. (1993) stated that this was the fourth example of a premature termination codon causing Stickler syndrome.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From EGL Genetic Diagnostics,Eurofins Clinical Diagnostics, SCV000336451.3

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

#	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		1	not provided	not provided	not provided

Last Updated: Nov 25, 2018

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