This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
ClinVar Genomic variation as it relates to human health
NM_001385875.1(ZFYVE27):c.805-5C>T
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.
(2)
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.
Conflicting classifications of pathogenicity
Uncertain significance(1); Likely benign(1)
Uncertain significance(1); Likely benign(1)
2
criteria provided, conflicting classifications
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_001385875.1(ZFYVE27):c.805-5C>T
Variation ID: 880086 Accession: VCV000880086.5
- Type and length
-
single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10q24.2 10: 97751386 (GRCh38) [ NCBI UCSC ] 10: 99511143 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 May 31, 2020 May 1, 2024 Aug 10, 2021 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001385875.1:c.805-5C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
intron variant NM_001002261.4:c.815C>T NP_001002261.1:p.Ser272Phe missense NM_001002262.4:c.805-5C>T intron variant NM_001174119.2:c.709-5C>T intron variant NM_001174120.2:c.547-5C>T intron variant NM_001174121.2:c.521C>T NP_001167592.1:p.Ser174Phe missense NM_001174122.2:c.451-5C>T intron variant NM_001385871.1:c.815C>T NP_001372800.1:p.Ser272Phe missense NM_001385876.1:c.854C>T NP_001372805.1:p.Ser285Phe missense NM_001385877.1:c.805-5C>T intron variant NM_001385878.1:c.815C>T NP_001372807.1:p.Ser272Phe missense NM_001385879.1:c.815C>T NP_001372808.1:p.Ser272Phe missense NM_001385880.1:c.805-5C>T intron variant NM_001385881.1:c.779C>T NP_001372810.1:p.Ser260Phe missense NM_001385882.1:c.815C>T NP_001372811.1:p.Ser272Phe missense NM_001385883.1:c.805-5C>T intron variant NM_001385884.1:c.805-5C>T intron variant NM_001385885.1:c.719C>T NP_001372814.1:p.Ser240Phe missense NM_001385886.1:c.719C>T NP_001372815.1:p.Ser240Phe missense NM_001385887.1:c.719C>T NP_001372816.1:p.Ser240Phe missense NM_001385888.1:c.719C>T NP_001372817.1:p.Ser240Phe missense NM_001385889.1:c.709-5C>T intron variant NM_001385890.1:c.611C>T NP_001372819.1:p.Ser204Phe missense NM_001385891.1:c.611C>T NP_001372820.1:p.Ser204Phe missense NM_001385892.1:c.601-5C>T intron variant NM_001385893.1:c.611C>T NP_001372822.1:p.Ser204Phe missense NM_001385894.1:c.611C>T NP_001372823.1:p.Ser204Phe missense NM_001385895.1:c.611C>T NP_001372824.1:p.Ser204Phe missense NM_001385896.1:c.601-5C>T intron variant NM_001385897.1:c.601-5C>T intron variant NM_001385898.1:c.601-5C>T intron variant NM_001385899.1:c.568-5C>T intron variant NM_001385900.1:c.568-5C>T intron variant NM_001385901.1:c.557C>T NP_001372830.1:p.Ser186Phe missense NM_001385902.1:c.557C>T NP_001372831.1:p.Ser186Phe missense NM_001385903.1:c.578C>T NP_001372832.1:p.Ser193Phe missense NM_001385904.1:c.578C>T NP_001372833.1:p.Ser193Phe missense NM_001385905.1:c.568-5C>T intron variant NM_001385906.1:c.547-5C>T intron variant NM_001385908.1:c.547-5C>T intron variant NM_001385911.1:c.557C>T NP_001372840.1:p.Ser186Phe missense NM_001385915.1:c.521C>T NP_001372844.1:p.Ser174Phe missense NM_001385916.1:c.472-5C>T intron variant NM_001385918.1:c.451-5C>T intron variant NM_001385919.1:c.172-5C>T intron variant NM_144588.7:c.805-5C>T intron variant NR_169798.1:n.974C>T non-coding transcript variant NR_169801.1:n.1010C>T non-coding transcript variant NR_169802.1:n.656C>T non-coding transcript variant NR_169806.1:n.999C>T non-coding transcript variant NR_169811.1:n.974C>T non-coding transcript variant NC_000010.11:g.97751386C>T NC_000010.10:g.99511143C>T NG_017075.1:g.19266C>T - Protein change
- S272F, S174F, S186F, S193F, S204F, S240F, S260F, S285F
- Other names
- -
- Canonical SPDI
- NC_000010.11:97751385:C:T
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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 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD) 0.00000
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00015
1000 Genomes Project 30x 0.00016
Exome Aggregation Consortium (ExAC) 0.00017
1000 Genomes Project 0.00020
- 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. |
|---|---|---|---|---|
| Likely benign (1) |
criteria provided, single submitter
|
Jan 13, 2018 | RCV001108096.4 | |
| Uncertain significance (1) |
criteria provided, single submitter
|
Aug 10, 2021 | RCV004032132.1 |
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. |
|
|---|---|---|---|---|---|
|
Likely benign
(Jan 13, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Hereditary spastic paraplegia 33
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV001265297.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. (less)
|
|
|
Uncertain significance
(Aug 10, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV004983593.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
The c.815C>T (p.S272F) alteration is located in exon 7 (coding exon 7) of the ZFYVE27 gene. This alteration results from a C to T substitution … (more)
The c.815C>T (p.S272F) alteration is located in exon 7 (coding exon 7) of the ZFYVE27 gene. This alteration results from a C to T substitution at nucleotide position 815, causing the serine (S) at amino acid position 272 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)
|
Comment:
Comment:
The c.815C>T (p.S272F) alteration is located in exon 7 (coding exon 7) of the ZFYVE27 gene. This alteration results from a C to T substitution at nucleotide position 815, causing the serine (S) at amino acid position 272 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
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:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Comment:
The c.815C>T (p.S272F) alteration is located in exon 7 (coding exon 7) of the ZFYVE27 gene. This alteration results from a C to T substitution at nucleotide position 815, causing the serine (S) at amino acid position 272 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
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 rs535449776 ...
HelpThese citations are identified by LitVar using
the rs number, so they may include citations for more than one variant
at this location. Please review the LitVar results carefully for your
variant of interest.
Record last updated Oct 08, 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.