ClinVar Genomic variation as it relates to human health
NM_002206.3(ITGA7):c.3268C>T (p.Gln1090Ter)
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_002206.3(ITGA7):c.3268C>T (p.Gln1090Ter)
Variation ID: 470579 Accession: VCV000470579.20
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 12q13.2 12: 56078988 (GRCh37) [ NCBI UCSC ] 12: 55685204 (GRCh38) [ 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 26, 2017 Apr 15, 2024 Apr 4, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_002206.3:c.3268C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_002197.2:p.Gln1090Ter nonsense NM_001144996.2:c.3280C>T NP_001138468.1:p.Gln1094Ter nonsense NM_001144997.2:c.2989C>T NP_001138469.1:p.Gln997Ter nonsense NM_001367993.1:c.2941C>T NP_001354922.1:p.Gln981Ter nonsense NM_001367994.1:c.1924C>T NP_001354923.1:p.Gln642Ter nonsense NM_001374465.1:c.3250C>T NP_001361394.1:p.Gln1084Ter nonsense NM_001410977.1:c.3400C>T NP_001397906.1:p.Gln1134Ter nonsense NM_001414029.1:c.3262C>T NP_001400958.1:p.Gln1088Ter nonsense NM_001414030.1:c.3193C>T NP_001400959.1:p.Gln1065Ter nonsense NM_001414031.1:c.3181C>T NP_001400960.1:p.Gln1061Ter nonsense NM_001414032.1:c.3148C>T NP_001400961.1:p.Gln1050Ter nonsense NM_001414033.1:c.3085C>T NP_001400962.1:p.Gln1029Ter nonsense NM_001414034.1:c.3043C>T NP_001400963.1:p.Gln1015Ter nonsense NM_001414035.1:c.2929C>T NP_001400964.1:p.Gln977Ter nonsense NC_000012.12:g.55685204G>A NC_000012.11:g.56078988G>A NG_012343.1:g.32102C>T LRG_871:g.32102C>T LRG_871t1:c.3268C>T LRG_871p1:p.Gln1090Ter LRG_871t2:c.2989C>T LRG_871p2:p.Gln997Ter - Protein change
- Q997*, Q1090*, Q1094*, Q642*, Q981*, Q1084*, Q1134*, Q1088*, Q1029*, Q1061*, Q1065*, Q1015*, Q977*, Q1050*
- Other names
- -
- Canonical SPDI
- NC_000012.12:55685203:G:A
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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.
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD) 0.00025
Trans-Omics for Precision Medicine (TOPMed) 0.00025
The Genome Aggregation Database (gnomAD), exomes 0.00029
Exome Aggregation Consortium (ExAC) 0.00031
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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ITGA7 | - | - |
GRCh38 GRCh37 |
827 | 978 |
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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Uncertain significance (5) |
criteria provided, multiple submitters, no conflicts
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Apr 4, 2024 | RCV000551016.17 | |
Uncertain significance (1) |
criteria provided, single submitter
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Jun 11, 2019 | RCV001576148.3 | |
Uncertain significance (1) |
criteria provided, single submitter
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May 18, 2022 | RCV002265798.1 |
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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Uncertain significance
(Feb 01, 2019)
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criteria provided, single submitter
Method: clinical testing
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Congenital muscular dystrophy due to integrin alpha-7 deficiency
Affected status: yes
Allele origin:
germline
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Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001429412.1
First in ClinVar: Aug 15, 2020 Last updated: Aug 15, 2020 |
Number of individuals with the variant: 1
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Uncertain significance
(Jun 11, 2019)
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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: SCV001803277.1
First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021 |
Comment:
Has not been previously published as pathogenic or benign to our knowledge; Nonsense variant predicted to result in protein truncation, although loss-of-function variants have not … (more)
Has not been previously published as pathogenic or benign to our knowledge; Nonsense variant predicted to result in protein truncation, although loss-of-function variants have not been reported downstream of this position in the protein (less)
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Uncertain significance
(May 18, 2022)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV002548229.1
First in ClinVar: Jul 18, 2022 Last updated: Jul 18, 2022 |
Comment:
Variant summary: ITGA7 c.3268C>T (p.Gln1090X) results in a premature termination codon. While not predicted cause nonsense mediated decay, this truncation removes the last 48 amino … (more)
Variant summary: ITGA7 c.3268C>T (p.Gln1090X) results in a premature termination codon. While not predicted cause nonsense mediated decay, this truncation removes the last 48 amino acids in the encoded protein sequence. Truncations downstream of this position have been classified as VUS within ClinVar (e.g. c.3316_3325del [p.Ser1106fs]). The variant allele was found at a frequency of 0.00029 in 251426 control chromosomes (gnomAD). To our knowledge, no occurrence of c.3268C>T in individuals affected with Congenital Muscular Dystrophy Due To Integrin Alpha-7 Deficiency and no experimental evidence demonstrating its impact on protein function have been reported. Four ClinVar submitters have assessed the variant since 2014: three classified the variant as of uncertain significance and one as likely pathogenic. Based on the evidence outlined above, the variant was classified as uncertain significance. (less)
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Uncertain significance
(Aug 31, 2022)
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criteria provided, single submitter
Method: clinical testing
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Congenital muscular dystrophy due to integrin alpha-7 deficiency
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000648333.6
First in ClinVar: Dec 26, 2017 Last updated: Feb 07, 2023 |
Comment:
This sequence change creates a premature translational stop signal (p.Gln1090*) in the ITGA7 gene. While this is not anticipated to result in nonsense mediated decay, … (more)
This sequence change creates a premature translational stop signal (p.Gln1090*) in the ITGA7 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 48 amino acid(s) of the ITGA7 protein. This variant is present in population databases (rs200390529, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with ITGA7-related conditions. ClinVar contains an entry for this variant (Variation ID: 470579). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
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Uncertain significance
(Dec 30, 2023)
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criteria provided, single submitter
Method: clinical testing
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Congenital muscular dystrophy due to integrin alpha-7 deficiency
Affected status: unknown
Allele origin:
inherited
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Genomic Research Center, Shahid Beheshti University of Medical Sciences
Accession: SCV000746344.2
First in ClinVar: Dec 26, 2017 Last updated: Jan 06, 2024 |
Age: 10-19 years
Sex: female
Geographic origin: Iran
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Uncertain significance
(Feb 27, 2023)
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criteria provided, single submitter
Method: clinical testing
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Congenital muscular dystrophy due to integrin alpha-7 deficiency
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV003813845.2
First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024 |
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Uncertain significance
(Apr 04, 2024)
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criteria provided, single submitter
Method: clinical testing
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Congenital muscular dystrophy due to integrin alpha-7 deficiency
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV004810128.1
First in ClinVar: Apr 15, 2024 Last updated: Apr 15, 2024 |
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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
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 rs200390529 ...
HelpRecord last updated Apr 15, 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.