ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.3967A>G (p.Ile1323Val)
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_000053.4(ATP7B):c.3967A>G (p.Ile1323Val)
Variation ID: 2075048 Accession: VCV002075048.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 13q14.3 13: 51937330 (GRCh38) [ NCBI UCSC ] 13: 52511466 (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 Feb 8, 2023 Feb 7, 2023 Jan 4, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000053.4:c.3967A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Ile1323Val missense NM_001005918.3:c.3346A>G NP_001005918.1:p.Ile1116Val missense NM_001243182.2:c.3634A>G NP_001230111.1:p.Ile1212Val missense NM_001330578.2:c.3733A>G NP_001317507.1:p.Ile1245Val missense NM_001330579.2:c.3715A>G NP_001317508.1:p.Ile1239Val missense NM_001406511.1:c.3967A>G NP_001393440.1:p.Ile1323Val missense NM_001406512.1:c.3967A>G NP_001393441.1:p.Ile1323Val missense NM_001406513.1:c.3961A>G NP_001393442.1:p.Ile1321Val missense NM_001406514.1:c.3934A>G NP_001393443.1:p.Ile1312Val missense NM_001406515.1:c.3913A>G NP_001393444.1:p.Ile1305Val missense NM_001406516.1:c.3913A>G NP_001393445.1:p.Ile1305Val missense NM_001406517.1:c.3871A>G NP_001393446.1:p.Ile1291Val missense NM_001406518.1:c.3871A>G NP_001393447.1:p.Ile1291Val missense NM_001406519.1:c.3832A>G NP_001393448.1:p.Ile1278Val missense NM_001406520.1:c.3823A>G NP_001393449.1:p.Ile1275Val missense NM_001406521.1:c.3823A>G NP_001393450.1:p.Ile1275Val missense NM_001406522.1:c.3823A>G NP_001393451.1:p.Ile1275Val missense NM_001406523.1:c.3784A>G NP_001393452.1:p.Ile1262Val missense NM_001406524.1:c.3790A>G NP_001393453.1:p.Ile1264Val missense NM_001406525.1:c.3772A>G NP_001393454.1:p.Ile1258Val missense NM_001406526.1:c.3763A>G NP_001393455.1:p.Ile1255Val missense NM_001406527.1:c.3733A>G NP_001393456.1:p.Ile1245Val missense NM_001406528.1:c.3733A>G NP_001393457.1:p.Ile1245Val missense NM_001406530.1:c.3727A>G NP_001393459.1:p.Ile1243Val missense NM_001406531.1:c.3715A>G NP_001393460.1:p.Ile1239Val missense NM_001406532.1:c.3715A>G NP_001393461.1:p.Ile1239Val missense NM_001406534.1:c.3679A>G NP_001393463.1:p.Ile1227Val missense NM_001406535.1:c.3637A>G NP_001393464.1:p.Ile1213Val missense NM_001406536.1:c.3637A>G NP_001393465.1:p.Ile1213Val missense NM_001406537.1:c.3628A>G NP_001393466.1:p.Ile1210Val missense NM_001406538.1:c.3589A>G NP_001393467.1:p.Ile1197Val missense NM_001406539.1:c.3538A>G NP_001393468.1:p.Ile1180Val missense NM_001406540.1:c.3520A>G NP_001393469.1:p.Ile1174Val missense NM_001406541.1:c.3481A>G NP_001393470.1:p.Ile1161Val missense NM_001406542.1:c.3481A>G NP_001393471.1:p.Ile1161Val missense NM_001406543.1:c.3475A>G NP_001393472.1:p.Ile1159Val missense NM_001406544.1:c.3385A>G NP_001393473.1:p.Ile1129Val missense NM_001406545.1:c.3319A>G NP_001393474.1:p.Ile1107Val missense NM_001406546.1:c.3286A>G NP_001393475.1:p.Ile1096Val missense NM_001406547.1:c.3124A>G NP_001393476.1:p.Ile1042Val missense NM_001406548.1:c.2677A>G NP_001393477.1:p.Ile893Val missense NC_000013.11:g.51937330T>C NC_000013.10:g.52511466T>C NG_008806.1:g.79165A>G - Protein change
- I1129V, I1210V, I1264V, I1278V, I1096V, I1107V, I1180V, I1197V, I1227V, I1255V, I1275V, I1312V, I1323V, I1116V, I1174V, I1212V, I1213V, I1239V, I1258V, I1262V, I1291V, I1305V, I1042V, I1159V, I1161V, I1243V, I1245V, I1321V, I893V
- Other names
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- Canonical SPDI
- NC_000013.11:51937329:T:C
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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
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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
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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
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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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ATP7B | - | - |
GRCh38 GRCh37 |
2886 | 3028 |
Conditions - Germline
Condition
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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
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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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Uncertain significance (1) |
criteria provided, single submitter
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Jan 4, 2022 | RCV002963242.1 |
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
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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
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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
(Jan 04, 2022)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV003289483.1
First in ClinVar: Feb 07, 2023 Last updated: Feb 07, 2023 |
Comment:
This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1323 of the ATP7B protein (p.Ile1323Val). … (more)
This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1323 of the ATP7B protein (p.Ile1323Val). This variant is present in population databases (rs377334296, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with ATP7B-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ATP7B protein function. 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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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 this variant ...
HelpRecord last updated Feb 13, 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.