ClinVar Genomic variation as it relates to human health
NM_003465.3(CHIT1):c.304G>A (p.Gly102Ser)
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.
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_003465.3(CHIT1):c.304G>A (p.Gly102Ser)
Variation ID: 9526 Accession: VCV000009526.17
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1q32.1 1: 203225058 (GRCh38) [ NCBI UCSC ] 1: 203194186 (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 Dec 6, 2016 Mar 10, 2024 Mar 10, 2020 - HGVS
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Nucleotide Protein Molecular
consequenceNM_003465.3:c.304G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_003456.1:p.Gly102Ser missense NM_001256125.2:c.257+611G>A intron variant NR_045784.2:n.341G>A non-coding transcript variant NR_045785.2:n.341G>A non-coding transcript variant NC_000001.11:g.203225058C>T NC_000001.10:g.203194186C>T NG_012867.1:g.9675G>A Q13231:p.Gly102Ser - Protein change
- G102S
- Other names
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- Canonical SPDI
- NC_000001.11:203225057:C:T
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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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0.29093 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
1000 Genomes Project 30x 0.28732
1000 Genomes Project 0.29093
Trans-Omics for Precision Medicine (TOPMed) 0.29368
The Genome Aggregation Database (gnomAD) 0.29831
Exome Aggregation Consortium (ExAC) 0.30231
The Genome Aggregation Database (gnomAD), exomes 0.30505
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 | ||
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HI score
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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. |
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CHIT1 | - | - |
GRCh38 GRCh37 |
188 | 204 |
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. |
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Benign (3) |
criteria provided, multiple submitters, no conflicts
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Dec 20, 2019 | RCV000010134.17 | |
Benign (3) |
criteria provided, single submitter
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Mar 10, 2020 | RCV000675725.8 |
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
Help
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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Benign
(Mar 06, 2018)
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criteria provided, single submitter
Method: clinical testing
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Chitotriosidase deficiency
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000353426.3
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)
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Benign
(Mar 10, 2020)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001950665.2
First in ClinVar: Oct 02, 2021 Last updated: Mar 04, 2023 |
Comment:
This variant is associated with the following publications: (PMID: 24060732, 19725875, 17000706)
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Benign
(Dec 20, 2019)
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criteria provided, single submitter
Method: clinical testing
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Chitotriosidase deficiency
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000837660.4
First in ClinVar: Oct 10, 2018 Last updated: May 04, 2020 |
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Uncertain significance
(Oct 22, 2015)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000801439.1
First in ClinVar: Aug 05, 2018 Last updated: Aug 05, 2018 |
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Affects
(Sep 01, 2007)
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no assertion criteria provided
Method: literature only
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CHITOTRIOSIDASE DEFICIENCY
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000030355.3
First in ClinVar: Apr 04, 2013 Last updated: Mar 10, 2024 |
Comment on evidence:
In 3 Ashkenazi Jewish type I Gaucher disease (230800) patients with chitotriosidase deficiency (CHITD; 614122), Grace et al. (2007) identified a 304G-A transition in exon … (more)
In 3 Ashkenazi Jewish type I Gaucher disease (230800) patients with chitotriosidase deficiency (CHITD; 614122), Grace et al. (2007) identified a 304G-A transition in exon 4 of the CHIT1 gene, resulting in a gly102-to-ser (G102S) substitution. In vitro functional expression studies showed that the G102S mutant had 23% activity compared to control values. The G102S allele had a frequency of 0.2 to 0.3 in various control populations. (less)
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not provided
(-)
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no classification provided
Method: phenotyping only
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Not Provided
Affected status: unknown
Allele origin:
unknown
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GenomeConnect - Invitae Patient Insights Network
Accession: SCV001749724.1
First in ClinVar: Jul 18, 2021 Last updated: Jul 18, 2021 |
Comment:
Variant interpreted as Benign and reported on 11-13-2019 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report … (more)
Variant interpreted as Benign and reported on 11-13-2019 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. (less)
Clinical Features:
Autoimmunity (present) , Immunodeficiency (present) , Abnormal inflammatory response (present) , Abnormal stomach morphology (present) , Abnormality of reproductive system physiology (present) , Abnormality of … (more)
Autoimmunity (present) , Immunodeficiency (present) , Abnormal inflammatory response (present) , Abnormal stomach morphology (present) , Abnormality of reproductive system physiology (present) , Abnormality of the nervous system (present) , Cognitive impairment (present) , Abnormality of coordination (present) , Memory impairment (present) , Anxiety (present) (less)
Indication for testing: Diagnostic
Age: 30-39 years
Sex: male
Testing laboratory: Invitae
Date variant was reported to submitter: 2019-11-13
Testing laboratory interpretation: Benign
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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. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Type 1 Gaucher disease: null and hypomorphic novel chitotriosidase mutations-implications for diagnosis and therapeutic monitoring. | Grace ME | Human mutation | 2007 | PMID: 17464953 |
Text-mined citations for rs2297950 ...
HelpRecord last updated Mar 11, 2024
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.