ClinVar Genomic variation as it relates to human health
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- Interpretation:
-
Pathogenic
- Review status:
- no assertion criteria provided
- Submissions:
- 2
- First in ClinVar:
- Sep 28, 2019
- Most recent Submission:
- Dec 31, 2019
- Last evaluated:
- Dec 23, 2019
- Accession:
- VCV000690370.2
- Variation ID:
- 690370
- Description:
- 1bp duplication
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NM_032536.4(NTNG2):c.376dup (p.Ser126fs)
- Allele ID
- 678055
- Variant type
- Duplication
- Variant length
- 1 bp
- Cytogenetic location
- 9q34.13
- Genomic location
- 9: 132198125-132198126 (GRCh38) GRCh38 UCSC
- 9: 135073512-135073513 (GRCh37) GRCh37 UCSC
- HGVS
-
Nucleotide Protein Molecular
consequenceNM_032536.4:c.376dup MANE Select NP_115925.2:p.Ser126fs frameshift NC_000009.12:g.132198128dup NC_000009.11:g.135073515dup - Protein change
- S126fs
- Other names
- -
- Canonical SPDI
- NC_000009.12:132198125:TTT:TTTT
- Functional consequence
- protein loss of function [Variation Ontology VariO:0043]
- Global minor allele frequency (GMAF)
- -
- Allele frequency
- -
- Links
- OMIM: 618689.0001
- dbSNP: rs1589441428
- 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 | Aug 19, 2019 | RCV000851301.1 | |
| Pathogenic | 1 | no assertion criteria provided | Dec 23, 2019 | RCV000984633.1 |
Submitted interpretations and evidence
Help| Interpretation (Last evaluated) |
Review status (Assertion criteria) |
Condition (Inheritance) |
Submitter | More information | |
|---|---|---|---|---|---|
|
Pathogenic
(Aug 19, 2019)
|
no assertion criteria provided
Method: clinical testing
|
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
inherited
|
Clinical Genomics Unit, Sheba Medical Center
Accession: SCV000965677.1
First in ClinVar: Sep 28, 2019 Last updated: Sep 28, 2019 |
Zygosity: 1 Homozygote
Sex: female
Ethnicity/Population group: Muslim
Geographic origin: Israel
|
|
|
Pathogenic
(Dec 23, 2019)
|
no assertion criteria provided
Method: literature only
|
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV001132675.1
First in ClinVar: Dec 31, 2019 Last updated: Dec 31, 2019 |
Comment on evidence:
In 8 patients from 4 consanguineous Arab Muslim families with neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia (NEDBASH; 618718), Abu-Libdeh et al. (2019) … (more)
In 8 patients from 4 consanguineous Arab Muslim families with neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia (NEDBASH; 618718), Abu-Libdeh et al. (2019) identified a homozygous 1-bp duplication (c.376dupT, NM_032536.3) in the NTNG2 gene, resulting in a frameshift and premature termination (Ser126PhefsTer241). The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in all families. Haplotype analysis indicated a founder effect. The mutation was not found in the gnomAD database, but the heterozygous variant was found in 2 of about 3,500 individuals in an in-house database of mainly Arab Muslim individuals. Functional studies of the variant and studies of patient cells were not performed, but the variant was predicted to result in a loss of function. Heimer et al. (2019) identified homozygosity for the c.376dupT mutation in exon 3 of the NTNG2 gene in 3 patients from 2 consanguineous Arab Muslim families with NEDBASH. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in both families. Functional studies of the variant and studies of patient cells were not performed, but the mutation was predicted to result in nonsense-mediated mRNA decay and a loss of function. (less)
|
Functional evidence
Help| Functional consequence | Method | Result | Submitter | More information |
|---|---|---|---|---|
|
protein loss of function
|
Clinical Genomics Unit, Sheba Medical Center
Accession: SCV000965677.1
First in ClinVar: Sep 28, 2019
Last updated: Sep 28, 2019
|
|
Citations for this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Netrin-G2 dysfunction causes a Rett-like phenotype with areflexia. | Heimer G | Human mutation | 2020 | PMID: 31692205 |
| Homozygous frameshift variant in NTNG2, encoding a synaptic cell adhesion molecule, in individuals with developmental delay, hypotonia, and autistic features. | Abu-Libdeh B | Neurogenetics | 2019 | PMID: 31372774 |
Text-mined citations for rs1589441428...
HelpThese citations are identified by LitVar using
the rs number, so they may include citations for more than one variant
at this location. Please review the LitVar results carefully for your
variant of interest.
Record last updated Aug 13, 2023