Pathogenic homozygous deletion based on previous publications
ClinVar Genomic variation as it relates to human health
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- Interpretation:
-
Pathogenic
- Review status:
- no assertion criteria provided
- Submissions:
- 1
- First in ClinVar:
- Dec 26, 2017
- Most recent Submission:
- Dec 26, 2017
- Last evaluated:
- Jun 20, 2016
- Accession:
- VCV000453297.3
- Variation ID:
- 453297
- Description:
- 122.1kb deletion
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Single allele
- Allele ID
- 446900
- Variant type
- Deletion
- Variant length
- 122,143 bp
- Cytogenetic location
- 2q13
- Genomic location
- 2: 110095383-110217525 (GRCh38) GRCh38 UCSC
- 2: 110852960-110975102 (GRCh37) GRCh37 UCSC
- HGVS
-
Nucleotide Protein Molecular
consequenceNC_000002.12:g.110095383_110217525del NC_000002.11:g.110852960_110975102del - Protein change
- -
- Other names
- -
- Canonical SPDI
- -
- Functional consequence
- -
- Global minor allele frequency (GMAF)
- -
- Allele frequency
- -
- Links
- VarSome
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Aggregate interpretations per condition
| Interpreted condition | Interpretation | Number of submissions | Review status | Last evaluated | Variation/condition record |
|---|---|---|---|---|---|
| Pathogenic | 1 | no assertion criteria provided | Jun 20, 2016 | RCV000529276.3 |
Clinical features observed in individuals with this variant
- Wide nasal bridge
- Wide intermamillary distance
- Visual impairment
- Toe syndactyly
- Thoracic scoliosis
- Thoracic kyphosis
- Stage 5 chronic kidney disease
- Secondary hyperparathyroidism
- Scoliosis
- Retinal dystrophy
- Pes planus
- Nystagmus
- Nephronophthisis
- Moderate visual impairment
- Macrocephaly
- Long philtrum
- Kyphosis
- Hypertension
- Hand tremor
- Few cafe-au-lait spots
- Exotropia
- Dysmetria
- Dysdiadochokinesis
- Delayed speech and language development
- Delayed gross motor development
- Deeply set eye
- Cone/cone-rod dystrophy
- Barrel-shaped chest
- Cerebellar ataxia
- Abnormality of the vertebral column
- Abnormality of the sixth cranial nerve
- Abnormal electroretinogram
- 2-3 toe syndactyly
Help
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation | Variation viewer | Related variants | ||
|---|---|---|---|---|---|---|
| HI score Help | TS score Help | Within gene | All | |||
| LOC126806305 | - | - | - | GRCh38 | - | 53 |
| LOC126806306 | - | - | - | GRCh38 | - | 76 |
| LOC129934555 | - | - | - | GRCh38 | - | 32 |
| LOC129934556 | - | - | - | GRCh38 | - | 30 |
| MALL | - | - |
GRCh38 GRCh37 |
1 | 163 | |
| MTLN | - | - | - | GRCh38 | - | 32 |
| NPHP1 | - | - |
GRCh38 GRCh37 |
631 | 815 | |
Submitted interpretations and evidence
Help| Interpretation (Last evaluated) |
Review status (Assertion criteria) |
Condition (Inheritance) |
Submitter | More information | |
|---|---|---|---|---|---|
|
Pathogenic
(Jun 20, 2016)
|
no assertion criteria provided
Method: clinical testing
|
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
inherited
|
Undiagnosed Diseases Network, NIH
Accession: SCV000622159.2
First in ClinVar: Dec 26, 2017 Last updated: Dec 26, 2017 |
Comment:
Pathogenic homozygous deletion based on previous publications
Clinical Features:
Wide nasal bridge (present) , Wide intermamillary distance (present) , Visual impairment (present) , Toe syndactyly (present) , Thoracic scoliosis (present) , Thoracic kyphosis (present) … (more)
Wide nasal bridge (present) , Wide intermamillary distance (present) , Visual impairment (present) , Toe syndactyly (present) , Thoracic scoliosis (present) , Thoracic kyphosis (present) , Stage 5 chronic kidney disease (present) , Secondary hyperparathyroidism (present) , Scoliosis (present) , Retinal dystrophy (present) , Pes planus (present) , Nystagmus (present) , Nephronophthisis (present) , Moderate visual impairment (present) , Macrocephaly (present) , Long philtrum (present) , Kyphosis (present) , Hypertension (present) , Hand tremor (present) , Few cafe-au-lait spots (present) , Exotropia (present) , Dysmetria (present) , Dysdiadochokinesis (present) , Delayed speech and language development (present) , Delayed gross motor development (present) , Deeply set eye (present) , Cone/cone-rod dystrophy (present) , Barrel-shaped chest (present) , Cerebellar ataxia (present) , Abnormality of the vertebral column (present) , Abnormality of the sixth cranial nerve (present) , Abnormal electroretinogram (present) , 2-3 toe syndactyly (present) (less)
Zygosity: 1 Homozygote
Family history: no
Age: 10-19 years
Sex: male
Ethnicity/Population group: White
Testing laboratory: GeneDx
Date variant was reported to submitter: 2016-06-20
|
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 |
|---|---|---|---|---|
| A deletion distinct from the classical homologous recombination of juvenile nephronophthisis type 1 (NPH1) allows exact molecular definition of deletion breakpoints. | Otto E | Human mutation | 2000 | PMID: 10980528 |
| Children with ocular motor apraxia type Cogan carry deletions in the gene (NPHP1) for juvenile nephronophthisis. | Betz R | The Journal of pediatrics | 2000 | PMID: 10839884 |
Record last updated Oct 15, 2023