PS2, PM2, PP3
ClinVar Genomic variation as it relates to human health
NM_018723.4(RBFOX1):c.1189T>G (p.Tyr397Asp)
Germline
Classification
Help
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
(1)
Help
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Likely pathogenic
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_018723.4(RBFOX1):c.1189T>G (p.Tyr397Asp)
Variation ID: 2580160 Accession: VCV002580160.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 16p13.3 16: 7710740 (GRCh38) [ NCBI UCSC ] 16: 7760742 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Sep 23, 2023 Sep 23, 2023 Sep 20, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_018723.4:c.1189T>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_061193.2:p.Tyr397Asp missense NM_145893.3:c.*117T>G MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
3 prime UTR NM_001142333.2:c.1108T>G NP_001135805.1:p.Tyr370Asp missense NM_001142334.2:c.1189T>G NP_001135806.1:p.Tyr397Asp missense NM_001364800.2:c.*117T>G 3 prime UTR NM_001415887.1:c.*117T>G 3 prime UTR NM_001415888.1:c.1705T>G NP_001402817.1:p.Tyr569Asp missense NM_001415889.1:c.*1099T>G 3 prime UTR NM_001415890.1:c.*1099T>G 3 prime UTR NM_001415891.1:c.1318T>G NP_001402820.1:p.Tyr440Asp missense NM_001415892.1:c.1297T>G NP_001402821.1:p.Tyr433Asp missense NM_001415893.1:c.1264T>G NP_001402822.1:p.Tyr422Asp missense NM_001415894.1:c.*1169T>G 3 prime UTR NM_001415895.1:c.*117T>G 3 prime UTR NM_001415896.1:c.1249T>G NP_001402825.1:p.Tyr417Asp missense NM_001415897.1:c.1237T>G NP_001402826.1:p.Tyr413Asp missense NM_001415898.1:c.*117T>G 3 prime UTR NM_001415899.1:c.*1169T>G 3 prime UTR NM_001415900.1:c.1216T>G NP_001402829.1:p.Tyr406Asp missense NM_001415901.1:c.*117T>G 3 prime UTR NM_001415902.1:c.1195T>G NP_001402831.1:p.Tyr399Asp missense NM_001415903.1:c.1183T>G NP_001402832.1:p.Tyr395Asp missense NM_001415904.1:c.*117T>G 3 prime UTR NM_001415905.1:c.1171T>G NP_001402834.1:p.Tyr391Asp missense NM_001415906.1:c.1171T>G NP_001402835.1:p.Tyr391Asp missense NM_001415907.1:c.*117T>G 3 prime UTR NM_001415908.1:c.*117T>G 3 prime UTR NM_001415909.1:c.*117T>G 3 prime UTR NM_001415910.1:c.*117T>G 3 prime UTR NM_001415911.1:c.*117T>G 3 prime UTR NM_001415912.1:c.1123T>G NP_001402841.1:p.Tyr375Asp missense NM_001415913.1:c.*117T>G 3 prime UTR NM_001415914.1:c.*1169T>G 3 prime UTR NM_001415915.1:c.*117T>G 3 prime UTR NM_001415916.1:c.1096T>G NP_001402845.1:p.Tyr366Asp missense NM_001415917.1:c.*117T>G 3 prime UTR NM_145891.3:c.1252T>G NP_665898.1:p.Tyr418Asp missense NM_145892.3:c.1174T>G NP_665899.1:p.Tyr392Asp missense NC_000016.10:g.7710740T>G NC_000016.9:g.7760742T>G NG_011881.2:g.2475989T>G - Protein change
- Y366D, Y370D, Y375D, Y391D, Y392D, Y395D, Y397D, Y399D, Y406D, Y413D, Y417D, Y418D, Y422D, Y433D, Y440D, Y569D
- Other names
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- Canonical SPDI
- NC_000016.10:7710739:T:G
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
| RBFOX1 | Little evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
542 | 694 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Likely pathogenic (1) |
criteria provided, single submitter
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Sep 20, 2023 | RCV003329103.2 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Likely pathogenic
(Sep 20, 2023)
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criteria provided, single submitter
Method: clinical testing
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Intellectual developmental disorder
Affected status: yes
Allele origin:
de novo
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Laboratory of genome editing, Research Centre for Medical Genetics
Accession: SCV004035911.1
First in ClinVar: Sep 23, 2023 Last updated: Sep 23, 2023 |
Comment:
PS2, PM2, PP3
Clinical Features:
Intellectual disability (present) , Microcephaly (present) , Broad columella (present) , Breast hypertrophy (present) , Shield chest (present) , Small hand (present) , Clinodactyly of … (more)
Intellectual disability (present) , Microcephaly (present) , Broad columella (present) , Breast hypertrophy (present) , Shield chest (present) , Small hand (present) , Clinodactyly of the 5th finger (present) , Pes valgus (present) , Depressed nasal ridge (present) (less)
Age: 10-19 years
Sex: female
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Comment:
Germline Functional Evidence
| 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. |
Comment:
PS2, PM2, PP3
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Complex Diagnostics of Non-Specific Intellectual Developmental Disorder. | Levchenko O | International journal of molecular sciences | 2022 | PMID: 35887114 |
Text-mined citations for this variant ...
HelpRecord last updated Sep 30, 2023
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.