rs1553200431
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM4PP3PP5_Moderate
The NM_001854.4(COL11A1):c.4048_4065del(p.Ser1350_Pro1355del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Consequence
COL11A1
NM_001854.4 inframe_deletion
NM_001854.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.29
Genes affected
COL11A1 (HGNC:2186): (collagen type XI alpha 1 chain) This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Mutations in this gene are associated with type II Stickler syndrome and with Marshall syndrome. A single-nucleotide polymorphism in this gene is also associated with susceptibility to lumbar disc herniation. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_001854.4.
PP3
?
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
PP5
?
Variant 1-102912179-GTGGGCCAGCCTCACCAGA-G is Pathogenic according to our data. Variant chr1-102912179-GTGGGCCAGCCTCACCAGA-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 523552.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL11A1 | NM_001854.4 | c.4048_4065del | p.Ser1350_Pro1355del | inframe_deletion | 54/67 | ENST00000370096.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL11A1 | ENST00000370096.9 | c.4048_4065del | p.Ser1350_Pro1355del | inframe_deletion | 54/67 | 1 | NM_001854.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hypertelorism;C0027092:Myopia;C0240310:Hypoplasia of the maxilla;C0344530:Megalocornea;C0423113:Telecanthus;C0424503:Abnormal facial shape;C1854114:Short nose;C2981150:Cleft palate Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at