ClinVar Genomic variation as it relates to human health
NM_007315.4(STAT1):c.373-2A>C
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_007315.4(STAT1):c.373-2A>C
Variation ID: 1710090 Accession: VCV001710090.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2q32.2 2: 191001165 (GRCh38) [ NCBI UCSC ] 2: 191865891 (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 Oct 15, 2022 Oct 15, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_007315.4:c.373-2A>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
splice acceptor NM_001384880.1:c.373-2A>C splice acceptor NM_001384881.1:c.379-2A>C splice acceptor NM_001384882.1:c.373-2A>C splice acceptor NM_001384883.1:c.373-2A>C splice acceptor NM_001384884.1:c.379-2A>C splice acceptor NM_001384885.1:c.373-2A>C splice acceptor NM_001384886.1:c.373-2A>C splice acceptor NM_001384887.1:c.373-2A>C splice acceptor NM_001384888.1:c.373-2A>C splice acceptor NM_001384889.1:c.373-2A>C splice acceptor NM_001384890.1:c.373-1461A>C intron variant NM_001384891.1:c.409-2A>C splice acceptor NM_139266.3:c.373-2A>C splice acceptor NC_000002.12:g.191001165T>G NC_000002.11:g.191865891T>G NG_008294.1:g.18086A>C LRG_111:g.18086A>C - Protein change
- Other names
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- Canonical SPDI
- NC_000002.12:191001164:T:G
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- effect on RNA splicing function Variation Ontology [VariO:0397]
- sequence_variant_affecting_splicing Sequence Ontology [SO:1000071]
- Reverse transcription PCR with primers located in exons 5 and 7 of STAT1 revealed three products in the mutation carrier sample, while only one middle-length band was observed in all samples used as controls. Sanger sequencing of the respective PCR products confirmed that the middle band (205 bp) corresponds to a wild type variant, the upper band (385 bp) corresponds to aberrant splicing where an upstream splice acceptor site is used, resulting in retention of 174 bp of intronic sequence, and the lower band (115 bp) corresponds to the product in which exon 6 is skipped. [submitted by Laboratory of Human Genetics,Chiril Draganiuc Institute of Phthisiopneumology]
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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 | ||
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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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STAT1 | No evidence available | No evidence available |
GRCh38 GRCh37 |
617 | 660 |
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
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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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Pathogenic (1) |
criteria provided, single submitter
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- | RCV002290424.1 |
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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Pathogenic
(-)
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criteria provided, single submitter
Method: research, in vitro
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Mendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency
Immunodeficiency 31B (Autosomal unknown)
Affected status: not applicable, yes
Allele origin:
unknown,
not applicable
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Laboratory of Human Genetics, Chiril Draganiuc Institute of Phthisiopneumology
Accession: SCV002581932.1
First in ClinVar: Oct 15, 2022 Last updated: Oct 15, 2022 |
Observation 1:
Number of individuals with the variant: 1
Clinical Features:
Extrapulmonary tuberculosis (present) , Pneumonia (present)
Family history: no
Age: 0-9 years
Sex: male
Ethnicity/Population group: Caucasian
Geographic origin: Eastern Europe
Tissue: blood
Secondary finding: no
Method: reverse transcription PCR
Observation 2:
Tissue: blood
Method: reverse transcription PCR
Result:
Reverse transcription PCR with primers located in exons 5 and 7 of STAT1 revealed three products in the mutation carrier sample, while only one middle-length band was observed in all samples used as controls. Sanger sequencing of the respective PCR products confirmed that the middle band (205 bp) corresponds to a wild type variant, the upper band (385 bp) corresponds to aberrant splicing where an upstream splice acceptor site is used, resulting in retention of 174 bp of intronic sequence, and the lower band (115 bp) corresponds to the product in which exon 6 is skipped.
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Germline Functional Evidence
Functional
Help
The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence |
Method
Help
A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter. |
Result
Help
A brief description of the result of this method for 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 functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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sequence_variant_affecting_splicing
effect on RNA splicing function
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Laboratory of Human Genetics, Chiril Draganiuc Institute of Phthisiopneumology
Accession: SCV002581932.1
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Comment:
Reverse transcription PCR with primers located in exons 5 and 7 of STAT1 revealed three products in the mutation carrier sample, while only one middle-length … (more)
Reverse transcription PCR with primers located in exons 5 and 7 of STAT1 revealed three products in the mutation carrier sample, while only one middle-length band was observed in all samples used as controls. Sanger sequencing of the respective PCR products confirmed that the middle band (205 bp) corresponds to a wild type variant, the upper band (385 bp) corresponds to aberrant splicing where an upstream splice acceptor site is used, resulting in retention of 174 bp of intronic sequence, and the lower band (115 bp) corresponds to the product in which exon 6 is skipped. (less)
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Citations for germline classification of this variant
HelpThere are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated Jun 10, 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.