chr19-18786034-T-TGTCGTC

Variant names:

• chr19-18786034-T-TGTCGTC
• rs193922900
• NM_000095.3:c.1414_1419dupGACGAC

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 5P and 1B. PM1 PM2 PP5 BP3

The NM_000095.3(COMP):​c.1414_1419dupGACGAC​(p.Asp472_Asp473dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: COMP NM_000095.3 conservative_inframe_insertion
• Clinical Significance: Pathogenic/Likely pathogenic no assertion criteria provided P:2
• Conservation: PhyloP100: 1.28
• Publications: 2 publications found

Genes affected

COMP (HGNC:2227): (cartilage oligomeric matrix protein) The protein encoded by this gene is a noncollagenous extracellular matrix (ECM) protein. It consists of five identical glycoprotein subunits, each with EGF-like and calcium-binding (thrombospondin-like) domains. Oligomerization results from formation of a five-stranded coiled coil and disulfides. Binding to other ECM proteins such as collagen appears to depend on divalent cations. Contraction or expansion of a 5 aa aspartate repeat and other mutations can cause pseudochondroplasia (PSACH) and multiple epiphyseal dysplasia (MED). [provided by RefSeq, Jul 2016]

COMP Gene-Disease associations (from GenCC):

• multiple epiphyseal dysplasia

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• pseudoachondroplasia

  Inheritance: AD, Unknown Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: ClinGen, Orphanet, Labcorp Genetics (formerly Invitae), Illumina
• multiple epiphyseal dysplasia type 1

  Inheritance: AD Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P

ACMG classification

Our verdict: Uncertain_significance. The variant received 4 ACMG points.

• PM1: In a hotspot region, there are 10 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 7 uncertain in NM_000095.3
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 19-18786034-T-TGTCGTC is Pathogenic according to our data. Variant chr19-18786034-T-TGTCGTC is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 9192.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP3: Nonframeshift variant in repetitive region in NM_000095.3

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COMP	NM_000095.3	c.1414_1419dupGACGAC	p.Asp472_Asp473dup	conservative_inframe_insertion	Exon 13 of 19	ENST00000222271.7	NP_000086.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COMP	ENST00000222271.7	c.1414_1419dupGACGAC	p.Asp472_Asp473dup	conservative_inframe_insertion	Exon 13 of 19	1	NM_000095.3	ENSP00000222271.2
COMP	ENST00000542601.6	c.1315_1320dupGACGAC	p.Asp439_Asp440dup	conservative_inframe_insertion	Exon 12 of 18	1		ENSP00000439156.2
COMP	ENST00000425807.1	c.1255_1260dupGACGAC	p.Asp419_Asp420dup	conservative_inframe_insertion	Exon 12 of 18	2		ENSP00000403792.1
COMP	ENST00000612179.1	n.*78_*83dupGACGAC		downstream_gene_variant		2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:2

Revision: no assertion criteria provided

Submissions by phenotype

COMP-related disorder Pathogenic:1

May 06, 2024

PreventionGenetics, part of Exact Sciences

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The COMP c.1414_1419dup6 variant is predicted to result in an in-frame duplication (p.Asp472_Asp473dup). This variant was reported in an individual with pseudoachondroplasia (Delot et al. 1999. PubMed ID: 9887340). This variant has not been reported in a large population database, indicating this variant is rare. Additionally, similar inframe deletions and duplications (p.Asp473dup, p.Asn474_Asp475dup, p.Asp473del) in this region have been documented as pathogenic in individuals with COMP-related disease (Delot et al. 1999. PubMed ID: 9887340; Briggs et al. 2014. PubMed ID: 24595329; Kim et al. 2021. PubMed ID: 34122524). This variant is interpreted as likely pathogenic. -

Pseudoachondroplastic spondyloepiphyseal dysplasia syndrome Pathogenic:1

Jan 01, 1999

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.3
Mutation Taster		=48/52	disease causing (ClinVar)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs193922900; hg19: chr19-18896844;