The variant segregated with strabismus in 5 affected members of a strabismus family, with an allele frequency lower than 0.1%, and minigene assay indicated that it enhances intron retention. Although gene function of OLFM3 involves development of the eyes and brains, direct evidence is still lacking to link the variant with strabismus.
ClinVar Genomic variation as it relates to human health
Help
- Interpretation:
-
Uncertain significance
- Review status:
- no assertion criteria provided
- Submissions:
- 1
- First in ClinVar:
- Nov 6, 2020
- Most recent Submission:
- Nov 6, 2020
- Last evaluated:
- Sep 1, 2020
- Accession:
- VCV000983485.2
- Variation ID:
- 983485
- Description:
- single nucleotide variant
Help
NM_058170.4(OLFM3):c.372+3A>G
- Allele ID
- 971551
- Variant type
- single nucleotide variant
- Variant length
- 1 bp
- Cytogenetic location
- 1p21.1
- Genomic location
- 1: 101830669 (GRCh38) GRCh38 UCSC
- 1: 102296225 (GRCh37) GRCh37 UCSC
- HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_058170.4:c.372+3A>G MANE Select intron variant NM_001288821.2:c.432+3A>G intron variant NM_001288823.2:c.147+3A>G intron variant NC_000001.11:g.101830669T>C NC_000001.10:g.102296225T>C - Protein change
- -
- Other names
- -
- Canonical SPDI
- NC_000001.11:101830668:T:C
- Functional consequence
- Variation affecting splicing function of RNA [Variation Ontology VariO:0397]
- Global minor allele frequency (GMAF)
- 0.00020 (C)
- Allele frequency
- Trans-Omics for Precision Medicine (TOPMed) 0.00002
- The Genome Aggregation Database (gnomAD), exomes 0.00003
- Trans-Omics for Precision Medicine (TOPMed) 0.00001
- 1000 Genomes Project 0.00020
- Exome Aggregation Consortium (ExAC) 0.00002
- Links
- dbSNP: rs566629297
- VarSome
Help
Aggregate interpretations per condition
| Interpreted condition | Interpretation | Number of submissions | Review status | Last evaluated | Variation/condition record |
|---|---|---|---|---|---|
| Uncertain significance | 1 | no assertion criteria provided | Sep 1, 2020 | RCV001263445.1 |
Submitted interpretations and evidence
Help| Interpretation (Last evaluated) |
Review status (Assertion criteria) |
Condition (Inheritance) |
Submitter | More information | |
|---|---|---|---|---|---|
|
Uncertain significance
(Sep 01, 2020)
|
no assertion criteria provided
Method: research
|
(Autosomal dominant inheritance)
Affected status: not applicable, yes
Allele origin:
germline,
not applicable
|
State Key Laboratory of Genetic Engineering, Fudan University
Accession: SCV001437973.1
First in ClinVar: Nov 06, 2020 Last updated: Nov 06, 2020 |
Comment:
The variant segregated with strabismus in 5 affected members of a strabismus family, with an allele frequency lower than 0.1%, and minigene assay indicated that … (more)
The variant segregated with strabismus in 5 affected members of a strabismus family, with an allele frequency lower than 0.1%, and minigene assay indicated that it enhances intron retention. Although gene function of OLFM3 involves development of the eyes and brains, direct evidence is still lacking to link the variant with strabismus. (less)
Observation 1:
Number of individuals with the variant: 6
Clinical Features:
Concomitant strabismus (present)
Zygosity: 0 Homozygote, 6 Single Heterozygote, 0 Compound Heterozygote, 0 Hemizygote
Sex: mixed
Ethnicity/Population group: East Asian
Geographic origin: China
Comment on evidence:
5 out of 6 carriers are affected with strabismus
Observation 2:
Result:
This variant enhances intron 3 retention from 10% to 30%. And the intron retention isoform is subject to NMD.
|
Functional evidence
Help| Functional consequence | Method | Result | Submitter | More information |
|---|---|---|---|---|
|
Variation affecting splicing function of RNA
|
|
|
State Key Laboratory of Genetic Engineering, Fudan University
Accession: SCV001437973.1
First in ClinVar: Nov 06, 2020
Last updated: Nov 06, 2020
|
|
Citations for this variant
Help| There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for rs566629297...
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 26, 2023