ClinVar Genomic variation as it relates to human health
NM_001385875.1(ZFYVE27):c.557A>G (p.Tyr186Cys)
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_001385875.1(ZFYVE27):c.557A>G (p.Tyr186Cys)
Variation ID: 570689 Accession: VCV000570689.19
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10q24.2 10: 97749479 (GRCh38) [ NCBI UCSC ] 10: 99509236 (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 10, 2018 Oct 20, 2024 Jan 1, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001385875.1:c.557A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001372804.1:p.Tyr186Cys missense NM_001002261.4:c.557A>G NP_001002261.1:p.Tyr186Cys missense NM_001002262.4:c.557A>G NP_001002262.1:p.Tyr186Cys missense NM_001174119.2:c.461A>G NP_001167590.1:p.Tyr154Cys missense NM_001174120.2:c.299A>G NP_001167591.1:p.Tyr100Cys missense NM_001174121.2:c.263A>G NP_001167592.1:p.Tyr88Cys missense NM_001174122.2:c.203A>G NP_001167593.1:p.Tyr68Cys missense NM_001385871.1:c.557A>G NP_001372800.1:p.Tyr186Cys missense NM_001385876.1:c.596A>G NP_001372805.1:p.Tyr199Cys missense NM_001385877.1:c.557A>G NP_001372806.1:p.Tyr186Cys missense NM_001385878.1:c.557A>G NP_001372807.1:p.Tyr186Cys missense NM_001385879.1:c.557A>G NP_001372808.1:p.Tyr186Cys missense NM_001385880.1:c.557A>G NP_001372809.1:p.Tyr186Cys missense NM_001385881.1:c.521A>G NP_001372810.1:p.Tyr174Cys missense NM_001385882.1:c.557A>G NP_001372811.1:p.Tyr186Cys missense NM_001385883.1:c.557A>G NP_001372812.1:p.Tyr186Cys missense NM_001385884.1:c.557A>G NP_001372813.1:p.Tyr186Cys missense NM_001385885.1:c.461A>G NP_001372814.1:p.Tyr154Cys missense NM_001385886.1:c.461A>G NP_001372815.1:p.Tyr154Cys missense NM_001385887.1:c.461A>G NP_001372816.1:p.Tyr154Cys missense NM_001385888.1:c.461A>G NP_001372817.1:p.Tyr154Cys missense NM_001385889.1:c.461A>G NP_001372818.1:p.Tyr154Cys missense NM_001385890.1:c.353A>G NP_001372819.1:p.Tyr118Cys missense NM_001385891.1:c.353A>G NP_001372820.1:p.Tyr118Cys missense NM_001385892.1:c.353A>G NP_001372821.1:p.Tyr118Cys missense NM_001385893.1:c.353A>G NP_001372822.1:p.Tyr118Cys missense NM_001385894.1:c.353A>G NP_001372823.1:p.Tyr118Cys missense NM_001385895.1:c.353A>G NP_001372824.1:p.Tyr118Cys missense NM_001385896.1:c.353A>G NP_001372825.1:p.Tyr118Cys missense NM_001385897.1:c.353A>G NP_001372826.1:p.Tyr118Cys missense NM_001385898.1:c.353A>G NP_001372827.1:p.Tyr118Cys missense NM_001385899.1:c.320A>G NP_001372828.1:p.Tyr107Cys missense NM_001385900.1:c.320A>G NP_001372829.1:p.Tyr107Cys missense NM_001385901.1:c.299A>G NP_001372830.1:p.Tyr100Cys missense NM_001385902.1:c.299A>G NP_001372831.1:p.Tyr100Cys missense NM_001385903.1:c.320A>G NP_001372832.1:p.Tyr107Cys missense NM_001385904.1:c.320A>G NP_001372833.1:p.Tyr107Cys missense NM_001385905.1:c.320A>G NP_001372834.1:p.Tyr107Cys missense NM_001385906.1:c.299A>G NP_001372835.1:p.Tyr100Cys missense NM_001385908.1:c.299A>G NP_001372837.1:p.Tyr100Cys missense NM_001385911.1:c.299A>G NP_001372840.1:p.Tyr100Cys missense NM_001385915.1:c.263A>G NP_001372844.1:p.Tyr88Cys missense NM_001385916.1:c.224A>G NP_001372845.1:p.Tyr75Cys missense NM_001385918.1:c.203A>G NP_001372847.1:p.Tyr68Cys missense NM_001385919.1:c.32-852A>G intron variant NM_144588.7:c.557A>G NP_653189.3:p.Tyr186Cys missense NR_169794.1:n.727A>G non-coding transcript variant NR_169795.1:n.685A>G non-coding transcript variant NR_169796.1:n.752A>G non-coding transcript variant NR_169798.1:n.716A>G non-coding transcript variant NR_169799.1:n.373A>G non-coding transcript variant NR_169801.1:n.752A>G non-coding transcript variant NR_169802.1:n.398A>G non-coding transcript variant NR_169803.1:n.727A>G non-coding transcript variant NR_169804.1:n.745A>G non-coding transcript variant NR_169805.1:n.756A>G non-coding transcript variant NR_169806.1:n.741A>G non-coding transcript variant NR_169808.1:n.784A>G non-coding transcript variant NR_169809.1:n.681A>G non-coding transcript variant NR_169810.1:n.752A>G non-coding transcript variant NR_169811.1:n.716A>G non-coding transcript variant NC_000010.11:g.97749479A>G NC_000010.10:g.99509236A>G NG_017075.1:g.17359A>G - Protein change
- Y186C, Y88C, Y100C, Y154C, Y68C, Y107C, Y118C, Y174C, Y199C, Y75C
- Other names
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- Canonical SPDI
- NC_000010.11:97749478:A:G
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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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0.00020 (G)
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Allele frequency
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The frequency of the allele represented by this VCV record.
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Exome Aggregation Consortium (ExAC) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00004
The Genome Aggregation Database (gnomAD) 0.00006
1000 Genomes Project 0.00020
1000 Genomes Project 30x 0.00031
- 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
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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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ZFYVE27 | - | - |
GRCh38 GRCh37 |
189 | 212 |
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
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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Uncertain significance (1) |
criteria provided, single submitter
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Apr 15, 2022 | RCV000691610.10 | |
Uncertain significance (1) |
criteria provided, single submitter
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Jan 1, 2023 | RCV003424285.10 |
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
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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
(Apr 15, 2022)
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criteria provided, single submitter
Method: clinical testing
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Spastic paraplegia
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000819396.7
First in ClinVar: Oct 10, 2018 Last updated: Feb 14, 2024 |
Comment:
ClinVar contains an entry for this variant (Variation ID: 570689). In summary, the available evidence is currently insufficient to determine the role of this variant … (more)
ClinVar contains an entry for this variant (Variation ID: 570689). 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with ZFYVE27-related conditions. This variant is present in population databases (rs575306476, gnomAD 0.005%). This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 186 of the ZFYVE27 protein (p.Tyr186Cys). (less)
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Uncertain significance
(Jan 01, 2023)
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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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CeGaT Center for Human Genetics Tuebingen
Accession: SCV004127185.10
First in ClinVar: Nov 20, 2023 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 1
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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 rs575306476 ...
HelpRecord last updated Oct 20, 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.