In a patient with a very mild phenotype, a de novo 13q14.13-13q31.1 mosaic deletion has been identified. Deletions in these genomic regions are responsible of a wide phenotypic spectrum known as "13q deletion syndrome" (Allerderdice, et al., 1969, Tranebjaerg et al., 1988, Brown et al., 1993, Brown et al., 1995, Van Buggenhout et al., 1999, Ballarati et al., 2007). Based on literature evidences, this deletion meets the criteria to be classified as pathogenic (ACMG Guidelines, 2011). In summary, the mosaic condition of 13q deletion very likely explain the mild phenotype observed in the patient.
ClinVar Genomic variation as it relates to human health
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- Interpretation:
-
Pathogenic
- Review status:
- criteria provided, single submitter
- Submissions:
- 1
- First in ClinVar:
- Nov 25, 2018
- Most recent Submission:
- Nov 25, 2018
- Accession:
- VCV000545122.1
- Variation ID:
- 545122
- Description:
- 40.4Mb deletion
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NC_000013.11:g.46968080_87381985del40413906
- Allele ID
- 535386
- Variant type
- Deletion
- Variant length
- 40,413,906 bp
- Cytogenetic location
- 13q14.2-31.2
- Genomic location
- 13: 46968080-87381985 (GRCh38) GRCh38 UCSC
- HGVS
-
Nucleotide Protein Molecular
consequenceNC_000013.11:g.46968080_87381985del40413906 - Protein change
- -
- Other names
- -
- Canonical SPDI
- -
- Functional consequence
- -
- Global minor allele frequency (GMAF)
- -
- Allele frequency
- -
- Links
- VarSome
Help
Aggregate interpretations per condition
| Interpreted condition | Interpretation | Number of submissions | Review status | Last evaluated | Variation/condition record |
|---|---|---|---|---|---|
| Pathogenic | 1 | criteria provided, single submitter | - | RCV000721955.2 |
Help
There are 522 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh38).
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation | Variation viewer | Related variants | ||
|---|---|---|---|---|---|---|
| HI score Help | TS score Help | Within gene | All | |||
| RB1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
2779 | 2917 | |
| EDNRB | Little evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
70 | 316 | |
| PCDH9 | No evidence available | No evidence available |
GRCh38 GRCh37 |
46 | 128 | |
| ACOD1 | - | - |
GRCh38 GRCh37 |
5 | 71 | |
| ALG11 | - | - |
GRCh38 GRCh37 |
69 | 244 | |
| ARL11 | - | - |
GRCh38 GRCh37 |
10 | 76 | |
| ATP7B | - | - |
GRCh38 GRCh37 |
2166 | 2304 | |
| ATXN8OS | - | - |
GRCh38 GRCh37 |
4 | 87 | |
| BORA | - | - |
GRCh38 GRCh37 |
18 | 88 | |
| C13orf42 | - | - | - | GRCh38 | - | 30 |
There are 522 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh38).
Submitted interpretations and evidence
Help| Interpretation (Last evaluated) |
Review status (Assertion criteria) |
Condition (Inheritance) |
Submitter | More information | |
|---|---|---|---|---|---|
|
Pathogenic
(-)
|
criteria provided, single submitter
Method: research
|
Affected status: yes
Allele origin:
de novo
|
Medical Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano
Accession: SCV000748684.1
First in ClinVar: Nov 25, 2018 Last updated: Nov 25, 2018 |
Comment:
In a patient with a very mild phenotype, a de novo 13q14.13-13q31.1 mosaic deletion has been identified. Deletions in these genomic regions are responsible of … (more)
In a patient with a very mild phenotype, a de novo 13q14.13-13q31.1 mosaic deletion has been identified. Deletions in these genomic regions are responsible of a wide phenotypic spectrum known as "13q deletion syndrome" (Allerderdice, et al., 1969, Tranebjaerg et al., 1988, Brown et al., 1993, Brown et al., 1995, Van Buggenhout et al., 1999, Ballarati et al., 2007). Based on literature evidences, this deletion meets the criteria to be classified as pathogenic (ACMG Guidelines, 2011). In summary, the mosaic condition of 13q deletion very likely explain the mild phenotype observed in the patient. (less)
Clinical Features:
Dysgraphia (present) , Class I obesity (present) , Hyperactivity (present) , Dysphagia (present) , Sleep disturbance (present) , Round face (present) , Thick eyebrow (present) … (more)
Dysgraphia (present) , Class I obesity (present) , Hyperactivity (present) , Dysphagia (present) , Sleep disturbance (present) , Round face (present) , Thick eyebrow (present) , Hamartoma (present) (less)
Age: 10-19 years
Sex: male
Ethnicity/Population group: European
Geographic origin: Italy
|
Functional evidence
Help| There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| 13q mosaic deletion including RB1 associated to mild phenotype and no cancer outcome - case report and review of the literature. | Bestetti I | Molecular cytogenetics | 2018 | PMID: 30250511 |
Record last updated Oct 15, 2023