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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with ZFYVE27-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.02%). This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 139 of the ZFYVE27 protein (p.Arg139Pro).
ClinVar Genomic variation as it relates to human health
NM_001385875.1(ZFYVE27):c.416G>C (p.Arg139Pro)
Germline
Classification
Help
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.
(1)
Help
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.
Uncertain significance
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001385875.1(ZFYVE27):c.416G>C (p.Arg139Pro)
Variation ID: 2885854 Accession: VCV002885854.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10q24.2 10: 97744876 (GRCh38) [ NCBI UCSC ] 10: 99504633 (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 20, 2024 Feb 20, 2024 Aug 4, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001385875.1:c.416G>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001372804.1:p.Arg139Pro missense NM_001002261.4:c.416G>C NP_001002261.1:p.Arg139Pro missense NM_001002262.4:c.416G>C NP_001002262.1:p.Arg139Pro missense NM_001174119.2:c.320G>C NP_001167590.1:p.Arg107Pro missense NM_001174120.2:c.198-3393G>C intron variant NM_001174121.2:c.122G>C NP_001167592.1:p.Arg41Pro missense NM_001174122.2:c.198-4598G>C intron variant NM_001385871.1:c.416G>C NP_001372800.1:p.Arg139Pro missense NM_001385876.1:c.455G>C NP_001372805.1:p.Arg152Pro missense NM_001385877.1:c.416G>C NP_001372806.1:p.Arg139Pro missense NM_001385878.1:c.416G>C NP_001372807.1:p.Arg139Pro missense NM_001385879.1:c.416G>C NP_001372808.1:p.Arg139Pro missense NM_001385880.1:c.416G>C NP_001372809.1:p.Arg139Pro missense NM_001385881.1:c.380G>C NP_001372810.1:p.Arg127Pro missense NM_001385882.1:c.416G>C NP_001372811.1:p.Arg139Pro missense NM_001385883.1:c.416G>C NP_001372812.1:p.Arg139Pro missense NM_001385884.1:c.416G>C NP_001372813.1:p.Arg139Pro missense NM_001385885.1:c.320G>C NP_001372814.1:p.Arg107Pro missense NM_001385886.1:c.416G>C NP_001372815.1:p.Arg139Pro missense NM_001385887.1:c.320G>C NP_001372816.1:p.Arg107Pro missense NM_001385888.1:c.320G>C NP_001372817.1:p.Arg107Pro missense NM_001385889.1:c.416G>C NP_001372818.1:p.Arg139Pro missense NM_001385890.1:c.212G>C NP_001372819.1:p.Arg71Pro missense NM_001385891.1:c.212G>C NP_001372820.1:p.Arg71Pro missense NM_001385892.1:c.212G>C NP_001372821.1:p.Arg71Pro missense NM_001385893.1:c.212G>C NP_001372822.1:p.Arg71Pro missense NM_001385894.1:c.212G>C NP_001372823.1:p.Arg71Pro missense NM_001385895.1:c.212G>C NP_001372824.1:p.Arg71Pro missense NM_001385896.1:c.212G>C NP_001372825.1:p.Arg71Pro missense NM_001385897.1:c.212G>C NP_001372826.1:p.Arg71Pro missense NM_001385898.1:c.212G>C NP_001372827.1:p.Arg71Pro missense NM_001385899.1:c.179G>C NP_001372828.1:p.Arg60Pro missense NM_001385900.1:c.179G>C NP_001372829.1:p.Arg60Pro missense NM_001385901.1:c.198-3393G>C intron variant NM_001385902.1:c.198-3393G>C intron variant NM_001385903.1:c.179G>C NP_001372832.1:p.Arg60Pro missense NM_001385904.1:c.179G>C NP_001372833.1:p.Arg60Pro missense NM_001385905.1:c.179G>C NP_001372834.1:p.Arg60Pro missense NM_001385906.1:c.198-3393G>C intron variant NM_001385908.1:c.198-3393G>C intron variant NM_001385911.1:c.198-3393G>C intron variant NM_001385915.1:c.122G>C NP_001372844.1:p.Arg41Pro missense NM_001385916.1:c.179G>C NP_001372845.1:p.Arg60Pro missense NM_001385917.1:c.179G>C NP_001372846.1:p.Arg60Pro missense NM_001385918.1:c.198-4598G>C intron variant NM_001385919.1:c.32-5455G>C intron variant NM_144588.7:c.416G>C NP_653189.3:p.Arg139Pro missense NR_169794.1:n.586G>C non-coding transcript variant NR_169795.1:n.544G>C non-coding transcript variant NR_169796.1:n.611G>C non-coding transcript variant NR_169797.1:n.586G>C non-coding transcript variant NR_169798.1:n.586G>C non-coding transcript variant NR_169800.1:n.611G>C non-coding transcript variant NR_169801.1:n.611G>C non-coding transcript variant NR_169803.1:n.586G>C non-coding transcript variant NR_169804.1:n.615G>C non-coding transcript variant NR_169805.1:n.615G>C non-coding transcript variant NR_169806.1:n.611G>C non-coding transcript variant NR_169808.1:n.654G>C non-coding transcript variant NR_169809.1:n.540G>C non-coding transcript variant NR_169810.1:n.611G>C non-coding transcript variant NR_169811.1:n.586G>C non-coding transcript variant NC_000010.11:g.97744876G>C NC_000010.10:g.99504633G>C NG_017075.1:g.12756G>C - Protein change
- R127P, R139P, R60P, R41P, R107P, R152P, R71P
- Other names
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- Canonical SPDI
- NC_000010.11:97744875:G: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
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 | ||
|---|---|---|---|---|---|---|
| HI score
Help
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. |
|||
| ZFYVE27 | - | - |
GRCh38 GRCh37 |
189 | 212 | |
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. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
|
Aug 4, 2023 | RCV003750487.3 |
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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|---|---|---|---|---|---|
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Uncertain significance
(Aug 04, 2023)
|
criteria provided, single submitter
Method: clinical testing
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Spastic paraplegia
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004509745.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
Comment:
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 … (more)
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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with ZFYVE27-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.02%). This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 139 of the ZFYVE27 protein (p.Arg139Pro). (less)
|
Comment:
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. |
Comment:
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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with ZFYVE27-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.02%). This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 139 of the ZFYVE27 protein (p.Arg139Pro).
Citations for germline classification of this variant
Help| There 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 Sep 30, 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.