ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.3912G>T (p.Leu1304Phe)
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.3912G>T (p.Leu1304Phe)
Variation ID: 2137511 Accession: VCV002137511.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 13q14.3 13: 51937385 (GRCh38) [ NCBI UCSC ] 13: 52511521 (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 14, 2024 Sep 20, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000053.4:c.3912G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Leu1304Phe missense NM_001005918.3:c.3291G>T NP_001005918.1:p.Leu1097Phe missense NM_001243182.2:c.3579G>T NP_001230111.1:p.Leu1193Phe missense NM_001330578.2:c.3678G>T NP_001317507.1:p.Leu1226Phe missense NM_001330579.2:c.3660G>T NP_001317508.1:p.Leu1220Phe missense NM_001406511.1:c.3912G>T NP_001393440.1:p.Leu1304Phe missense NM_001406512.1:c.3912G>T NP_001393441.1:p.Leu1304Phe missense NM_001406513.1:c.3906G>T NP_001393442.1:p.Leu1302Phe missense NM_001406514.1:c.3879G>T NP_001393443.1:p.Leu1293Phe missense NM_001406515.1:c.3858G>T NP_001393444.1:p.Leu1286Phe missense NM_001406516.1:c.3858G>T NP_001393445.1:p.Leu1286Phe missense NM_001406517.1:c.3816G>T NP_001393446.1:p.Leu1272Phe missense NM_001406518.1:c.3816G>T NP_001393447.1:p.Leu1272Phe missense NM_001406519.1:c.3777G>T NP_001393448.1:p.Leu1259Phe missense NM_001406520.1:c.3768G>T NP_001393449.1:p.Leu1256Phe missense NM_001406521.1:c.3768G>T NP_001393450.1:p.Leu1256Phe missense NM_001406522.1:c.3768G>T NP_001393451.1:p.Leu1256Phe missense NM_001406523.1:c.3729G>T NP_001393452.1:p.Leu1243Phe missense NM_001406524.1:c.3735G>T NP_001393453.1:p.Leu1245Phe missense NM_001406525.1:c.3717G>T NP_001393454.1:p.Leu1239Phe missense NM_001406526.1:c.3708G>T NP_001393455.1:p.Leu1236Phe missense NM_001406527.1:c.3678G>T NP_001393456.1:p.Leu1226Phe missense NM_001406528.1:c.3678G>T NP_001393457.1:p.Leu1226Phe missense NM_001406530.1:c.3672G>T NP_001393459.1:p.Leu1224Phe missense NM_001406531.1:c.3660G>T NP_001393460.1:p.Leu1220Phe missense NM_001406532.1:c.3660G>T NP_001393461.1:p.Leu1220Phe missense NM_001406534.1:c.3624G>T NP_001393463.1:p.Leu1208Phe missense NM_001406535.1:c.3582G>T NP_001393464.1:p.Leu1194Phe missense NM_001406536.1:c.3582G>T NP_001393465.1:p.Leu1194Phe missense NM_001406537.1:c.3573G>T NP_001393466.1:p.Leu1191Phe missense NM_001406538.1:c.3534G>T NP_001393467.1:p.Leu1178Phe missense NM_001406539.1:c.3483G>T NP_001393468.1:p.Leu1161Phe missense NM_001406540.1:c.3465G>T NP_001393469.1:p.Leu1155Phe missense NM_001406541.1:c.3426G>T NP_001393470.1:p.Leu1142Phe missense NM_001406542.1:c.3426G>T NP_001393471.1:p.Leu1142Phe missense NM_001406543.1:c.3420G>T NP_001393472.1:p.Leu1140Phe missense NM_001406544.1:c.3330G>T NP_001393473.1:p.Leu1110Phe missense NM_001406545.1:c.3264G>T NP_001393474.1:p.Leu1088Phe missense NM_001406546.1:c.3231G>T NP_001393475.1:p.Leu1077Phe missense NM_001406547.1:c.3069G>T NP_001393476.1:p.Leu1023Phe missense NM_001406548.1:c.2622G>T NP_001393477.1:p.Leu874Phe missense NC_000013.11:g.51937385C>A NC_000013.10:g.52511521C>A NG_008806.1:g.79110G>T - Protein change
- L1193F, L1224F, L1239F, L1272F, L1293F, L874F, L1023F, L1088F, L1161F, L1194F, L1243F, L1256F, L1286F, L1110F, L1142F, L1178F, L1208F, L1236F, L1245F, L1259F, L1077F, L1097F, L1191F, L1220F, L1226F, L1302F, L1304F, L1140F, L1155F
- Other names
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- Canonical SPDI
- NC_000013.11:51937384:C: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
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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 |
2850 | 2991 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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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Likely pathogenic (1) |
criteria provided, single submitter
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Sep 20, 2022 | RCV003062591.2 |
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
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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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Likely pathogenic
(Sep 20, 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: SCV003442220.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 14, 2024 |
Comment:
In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has … (more)
In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. 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 expected to disrupt ATP7B protein function. This missense change has been observed in individual(s) with Wilson disease (PMID: 21610751; Invitae). This variant is present in population databases (rs748644391, gnomAD 0.003%). This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 1304 of the ATP7B protein (p.Leu1304Phe). (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
HelpTitle | Author | Journal | Year | Link |
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Clinical presentation and mutations in Danish patients with Wilson disease. | Møller LB | European journal of human genetics : EJHG | 2011 | PMID: 21610751 |
Text-mined citations for this variant ...
HelpRecord last updated Feb 14, 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.