This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
ClinVar Genomic variation as it relates to human health
Help
- Interpretation:
-
Conflicting interpretations of pathogenicity
Uncertain significance(1); Benign(6)
- Review status:
- criteria provided, conflicting interpretations
- Submissions:
- 8
- First in ClinVar:
- Jul 6, 2014
- Most recent Submission:
- May 13, 2023
- Last evaluated:
- Oct 22, 2022
- Accession:
- VCV000130055.19
- Variation ID:
- 130055
- Description:
- single nucleotide variant
Help
NM_178161.3(PTF1A):c.787T>C (p.Ser263Pro)
- Allele ID
- 135501
- Variant type
- single nucleotide variant
- Variant length
- 1 bp
- Cytogenetic location
- 10p12.2
- Genomic location
- 10: 23193706 (GRCh38) GRCh38 UCSC
- 10: 23482635 (GRCh37) GRCh37 UCSC
- HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_178161.3:c.787T>C MANE Select NP_835455.1:p.Ser263Pro missense NC_000010.11:g.23193706T>C NC_000010.10:g.23482635T>C NG_009798.1:g.6176T>C Q7RTS3:p.Ser263Pro - Protein change
- S263P
- Other names
- -
- Canonical SPDI
- NC_000010.11:23193705:T:C
- Functional consequence
- -
- Global minor allele frequency (GMAF)
- 0.37560 (T)
- Allele frequency
- The Genome Aggregation Database (gnomAD) 0.51132
- The Genome Aggregation Database (gnomAD) 0.51842
- Trans-Omics for Precision Medicine (TOPMed) 0.54157
- NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.51076
- 1000 Genomes Project 0.62440
- Trans-Omics for Precision Medicine (TOPMed) 0.54231
- Links
- ClinGen: CA154815
- UniProtKB: Q7RTS3#VAR_049548
- dbSNP: rs7918487
- VarSome
Help
Aggregate interpretations per condition
| Interpreted condition | Interpretation | Number of submissions | Review status | Last evaluated | Variation/condition record |
|---|---|---|---|---|---|
| Likely benign | 1 | no assertion criteria provided | - | RCV000118082.7 | |
| Benign | 1 | criteria provided, single submitter | May 28, 2019 | RCV000333285.4 | |
| Benign | 2 | criteria provided, multiple submitters, no conflicts | Nov 7, 2021 | RCV001093986.7 | |
| Benign | 2 | criteria provided, multiple submitters, no conflicts | Oct 22, 2022 | RCV001522641.8 | |
| Benign | 1 | criteria provided, single submitter | Nov 7, 2021 | RCV001795174.3 | |
| Uncertain significance | 1 | criteria provided, single submitter | - | RCV003226203.1 |
Submitted interpretations and evidence
Help| Interpretation (Last evaluated) |
Review status (Assertion criteria) |
Condition (Inheritance) |
Submitter | More information | |
|---|---|---|---|---|---|
|
Benign
(May 28, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
Affected status: unknown
Allele origin:
unknown
|
Mendelics
Accession: SCV001138010.1
First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020 |
|
|
|
Benign
(Jan 13, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000361881.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
|
|
Benign
(Nov 12, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV001949397.2
First in ClinVar: Oct 02, 2021 Last updated: Mar 04, 2023 |
|
|
|
Uncertain significance
(-)
|
criteria provided, single submitter
(K & H Uppaluri Personalized Medicine Clinic Variant Classification & Assertion Criteria_Updated V.1)
Method: research
|
Affected status: unknown
Allele origin:
unknown
|
Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic
Accession: SCV003915676.1
First in ClinVar: May 13, 2023 Last updated: May 13, 2023 |
Comment:
PTF1A gene is associated with neonatal onset diabetes due to pancreatic aplasia, leading to insulin dependence. It is associated with extra pancreatic manifestation of neurological … (more)
PTF1A gene is associated with neonatal onset diabetes due to pancreatic aplasia, leading to insulin dependence. It is associated with extra pancreatic manifestation of neurological impairment. However, more evidence is required to ascertain the the role of this particular variant rs7918487 in neonatal diabetes. (less)
|
|
|
Benign
(Nov 07, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Affected status: no
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV002033285.1
First in ClinVar: Dec 18, 2021 Last updated: Dec 18, 2021 |
|
|
|
Benign
(Nov 07, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Affected status: no
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV002033286.1
First in ClinVar: Dec 18, 2021 Last updated: Dec 18, 2021 |
|
|
|
Benign
(Oct 22, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Affected status: unknown
Allele origin:
germline
|
Invitae
Accession: SCV001732226.3
First in ClinVar: Jun 15, 2021 Last updated: Feb 07, 2023 |
|
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
|
Genetic Services Laboratory, University of Chicago
Accession: SCV000152414.2
First in ClinVar: May 17, 2014 Last updated: Jul 06, 2014 |
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. (less)
|
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 |
|---|---|---|---|---|
| Reduction of Ptf1a gene dosage causes pancreatic hypoplasia and diabetes in mice. | Fukuda A | Diabetes | 2008 | PMID: 18591390 |
| - | - | - | - | DOI: 10.5812/ijp.114059 |
Text-mined citations for rs7918487...
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 May 13, 2023