NM_001851.6(COL9A1):c.876+2dup AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 1, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001052368.9

Allele description [Variation Report for NM_001851.6(COL9A1):c.876+2dup]

NM_001851.6(COL9A1):c.876+2dup

Gene:

COL9A1:collagen type IX alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

6q13

Genomic location:

Preferred name:

NM_001851.6(COL9A1):c.876+2dup

HGVS:

NC_000006.12:g.70281388dup
NG_011654.1:g.26696dup
NM_001377289.1:c.147+2dup
NM_001377290.1:c.147+2dup
NM_001377291.1:c.876+2dup
NM_001851.6:c.876+2dupMANE SELECT
NM_078485.4:c.147+2dup
NC_000006.11:g.70991090_70991091insA
NC_000006.11:g.70991091dup
NM_001851.4:c.876+2dup
NM_001851.4:c.876+2dupT

Links:

OMIM: 120210.0001; dbSNP: rs672601329

NCBI 1000 Genomes Browser:

rs672601329

Molecular consequence:

NM_001377289.1:c.147+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001377290.1:c.147+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001377291.1:c.876+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001851.6:c.876+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_078485.4:c.147+2dup - splice donor variant - [Sequence Ontology: SO:0001575]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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transmembrane protein 225B isoform X1 [Homo sapiens]
transmembrane protein 225B isoform X1 [Homo sapiens]
gi|1370509348|ref|XP_024302389.1|

Protein
87436[uid] (1)
Taxonomy
granulocyte-macrophage colony-stimulating factor receptor subunit alpha isoform ...
granulocyte-macrophage colony-stimulating factor receptor subunit alpha isoform X5 [Homo sapiens]
gi|2217401132|ref|XP_047298674.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001216577	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 13, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 17576681, 9536098, 11565064, 28492532
SCV004159701	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Dec 1, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001216577

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 13, 2022)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV004159701

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Uncertain significance
(Dec 1, 2022)

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	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001216577.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change falls in intron 8 of the COL9A1 gene. It does not directly change the encoded amino acid sequence of the COL9A1 protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs672601329, gnomAD 0.04%). This variant has been observed in individual(s) with multiple epiphyseal dysplasia (PMID: 11565064). ClinVar contains an entry for this variant (Variation ID: 17194). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exons 8 and/or 10, but is expected to preserve the integrity of the reading-frame (PMID: 11565064). 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.

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV004159701.5

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

Description

COL9A1: PP3, PS3:Supporting

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

Last Updated: May 12, 2024

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