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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
ClinVar Genomic variation as it relates to human health
NM_001385875.1(ZFYVE27):c.62C>T (p.Ala21Val)
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.
(8)
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.
Benign/Likely benign
8
criteria provided, multiple submitters, no conflicts
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_001385875.1(ZFYVE27):c.62C>T (p.Ala21Val)
Variation ID: 220394 Accession: VCV000220394.34
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 10q24.2 10: 97738539 (GRCh38) [ NCBI UCSC ] 10: 99498296 (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 Dec 6, 2016 Oct 20, 2024 Jan 18, 2024 - HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001385875.1:c.62C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001372804.1:p.Ala21Val missense NM_001002261.4:c.62C>T NP_001002261.1:p.Ala21Val missense NM_001002262.4:c.62C>T NP_001002262.1:p.Ala21Val missense NM_001174119.2:c.62C>T NP_001167590.1:p.Ala21Val missense NM_001174120.2:c.62C>T NP_001167591.1:p.Ala21Val missense NM_001174121.2:c.-27+1218C>T intron variant NM_001174122.2:c.62C>T NP_001167593.1:p.Ala21Val missense NM_001385871.1:c.62C>T NP_001372800.1:p.Ala21Val missense NM_001385876.1:c.62C>T NP_001372805.1:p.Ala21Val missense NM_001385877.1:c.62C>T NP_001372806.1:p.Ala21Val missense NM_001385878.1:c.62C>T NP_001372807.1:p.Ala21Val missense NM_001385879.1:c.62C>T NP_001372808.1:p.Ala21Val missense NM_001385880.1:c.62C>T NP_001372809.1:p.Ala21Val missense NM_001385881.1:c.62C>T NP_001372810.1:p.Ala21Val missense NM_001385882.1:c.62C>T NP_001372811.1:p.Ala21Val missense NM_001385883.1:c.62C>T NP_001372812.1:p.Ala21Val missense NM_001385884.1:c.62C>T NP_001372813.1:p.Ala21Val missense NM_001385885.1:c.62C>T NP_001372814.1:p.Ala21Val missense NM_001385886.1:c.62C>T NP_001372815.1:p.Ala21Val missense NM_001385887.1:c.62C>T NP_001372816.1:p.Ala21Val missense NM_001385888.1:c.62C>T NP_001372817.1:p.Ala21Val missense NM_001385889.1:c.62C>T NP_001372818.1:p.Ala21Val missense NM_001385890.1:c.-118C>T 5 prime UTR NM_001385891.1:c.-8+1218C>T intron variant NM_001385892.1:c.-8+1218C>T intron variant NM_001385893.1:c.-118C>T 5 prime UTR NM_001385894.1:c.-8+1218C>T intron variant NM_001385895.1:c.-118C>T 5 prime UTR NM_001385896.1:c.-8+1218C>T intron variant NM_001385897.1:c.-118C>T 5 prime UTR NM_001385898.1:c.-118C>T 5 prime UTR NM_001385899.1:c.-105C>T 5 prime UTR NM_001385900.1:c.-105C>T 5 prime UTR NM_001385901.1:c.62C>T NP_001372830.1:p.Ala21Val missense NM_001385902.1:c.62C>T NP_001372831.1:p.Ala21Val missense NM_001385903.1:c.-105C>T 5 prime UTR NM_001385904.1:c.-105C>T 5 prime UTR NM_001385905.1:c.-105C>T 5 prime UTR NM_001385906.1:c.62C>T NP_001372835.1:p.Ala21Val missense NM_001385908.1:c.62C>T NP_001372837.1:p.Ala21Val missense NM_001385911.1:c.62C>T NP_001372840.1:p.Ala21Val missense NM_001385915.1:c.-133C>T 5 prime UTR NM_001385916.1:c.-105C>T 5 prime UTR NM_001385918.1:c.62C>T NP_001372847.1:p.Ala21Val missense NM_001385919.1:c.-105C>T 5 prime UTR NM_144588.7:c.62C>T NP_653189.3:p.Ala21Val missense NR_169794.1:n.257C>T non-coding transcript variant NR_169795.1:n.261C>T non-coding transcript variant NR_169796.1:n.257C>T non-coding transcript variant NR_169797.1:n.257C>T non-coding transcript variant NR_169798.1:n.257C>T non-coding transcript variant NR_169799.1:n.257C>T non-coding transcript variant NR_169800.1:n.257C>T non-coding transcript variant NR_169801.1:n.257C>T non-coding transcript variant NR_169802.1:n.257C>T non-coding transcript variant NR_169803.1:n.257C>T non-coding transcript variant NR_169804.1:n.261C>T non-coding transcript variant NR_169805.1:n.261C>T non-coding transcript variant NR_169806.1:n.257C>T non-coding transcript variant NR_169808.1:n.261C>T non-coding transcript variant NR_169809.1:n.257C>T non-coding transcript variant NR_169810.1:n.257C>T non-coding transcript variant NR_169811.1:n.257C>T non-coding transcript variant NC_000010.11:g.97738539C>T NC_000010.10:g.99498296C>T NG_017075.1:g.6419C>T - Protein change
- A21V
- Other names
- -
- Canonical SPDI
- NC_000010.11:97738538:C:T
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
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.
-
0.00240 (T)
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
1000 Genomes Project 30x 0.00219
1000 Genomes Project 0.00240
Trans-Omics for Precision Medicine (TOPMed) 0.00358
The Genome Aggregation Database (gnomAD) 0.00388
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00507
- 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. |
|---|---|---|---|---|
| Benign (1) |
criteria provided, single submitter
|
Jan 18, 2024 | RCV000204398.13 | |
| Benign/Likely benign (4) |
criteria provided, multiple submitters, no conflicts
|
Dec 5, 2021 | RCV000625083.8 | |
| Benign (2) |
criteria provided, single submitter
|
Jun 12, 2017 | RCV000593305.6 | |
| Benign (1) |
criteria provided, single submitter
|
Aug 1, 2022 | RCV002292489.15 |
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. |
|
|---|---|---|---|---|---|
|
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: SCV000366357.3
First in ClinVar: Dec 06, 2016 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
|
|
Benign
(Jan 18, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Spastic paraplegia
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000260895.9
First in ClinVar: Feb 02, 2016 Last updated: Feb 20, 2024 |
|
|
|
Benign
(Aug 01, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV002585243.15
First in ClinVar: Oct 22, 2022 Last updated: Oct 20, 2024 |
Comment:
ZFYVE27: BP4, BS1, BS2
Number of individuals with the variant: 1
|
|
|
Likely benign
(Jul 28, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Hereditary spastic paraplegia 33
Affected status: yes
Allele origin:
germline
|
Genome Diagnostics Laboratory, University Medical Center Utrecht
Study: VKGL Data-share Consensus
Accession: SCV000743717.1 First in ClinVar: Apr 20, 2018 Last updated: Apr 20, 2018 |
|
|
|
Likely benign
(Apr 20, 2016)
|
criteria provided, single submitter
Method: clinical testing
|
Hereditary spastic paraplegia 33
Affected status: yes
Allele origin:
germline
|
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Study: VKGL Data-share Consensus
Accession: SCV000745119.1 First in ClinVar: Apr 20, 2018 Last updated: Apr 20, 2018 |
|
|
|
Benign
(Jun 12, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000709278.2
First in ClinVar: Apr 02, 2018 Last updated: Apr 02, 2018 |
Number of individuals with the variant: 1
Sex: mixed
|
|
|
Benign
(Dec 05, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Hereditary spastic paraplegia 33
Affected status: no
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV002514151.1
First in ClinVar: May 21, 2022 Last updated: May 21, 2022 |
|
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV002036525.1 First in ClinVar: Dec 18, 2021 Last updated: Dec 18, 2021 |
|
Comment:
Comment:
ZFYVE27: BP4, BS1, BS2
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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Comment:
ZFYVE27: BP4, BS1, BS2
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ZFYVE27 | - | - | - | - |
Text-mined citations for rs140812293 ...
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 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.