ClinVar Genomic variation as it relates to human health
NM_001384140.1(PCDH15):c.4323_4328del (p.Pro1442_Pro1443del)
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_001384140.1(PCDH15):c.4323_4328del (p.Pro1442_Pro1443del)
Variation ID: 2136863 Accession: VCV002136863.2
- Type and length
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Deletion, 6 bp
- Location
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Cytogenetic: 10q21.1 10: 53827432-53827437 (GRCh38) [ NCBI UCSC ] 10: 55587192-55587197 (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 Jan 24, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001384140.1:c.4323_4328del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001371069.1:p.Pro1442_Pro1443del inframe deletion NM_033056.4:c.4323_4328del MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_149045.3:p.Pro1442_Pro1443del inframe deletion NM_001142763.2:c.4338_4343del NP_001136235.1:p.Pro1447_Pro1448del inframe deletion NM_001142764.2:c.4323_4328del NP_001136236.1:p.Pro1442_Pro1443del inframe deletion NM_001142765.2:c.4110_4115del NP_001136237.1:p.Pro1371_Pro1372del inframe deletion NM_001142766.2:c.4314_4319del NP_001136238.1:p.Pro1439_Pro1440del inframe deletion NM_001142767.2:c.4203_4208del NP_001136239.1:p.Pro1402_Pro1403del inframe deletion NM_001142768.2:c.4257_4262del NP_001136240.1:p.Pro1420_Pro1421del inframe deletion NM_001142769.3:c.4359_4364del NP_001136241.1:p.Pro1454_Pro1455del inframe deletion NM_001142770.3:c.4323_4328del NP_001136242.1:p.Pro1442_Pro1443del inframe deletion NM_001142771.2:c.4338_4343del NP_001136243.1:p.Pro1447_Pro1448del inframe deletion NM_001142772.2:c.4323_4328del NP_001136244.1:p.Pro1442_Pro1443del inframe deletion NM_001142773.2:c.4248_4253del NP_001136245.1:p.Pro1417_Pro1418del inframe deletion NM_001354404.2:c.4257_4262del NP_001341333.1:p.Pro1420_Pro1421del inframe deletion NM_001354411.2:c.4344_4349del NP_001341340.1:p.Pro1449_Pro1450del inframe deletion NM_001354420.2:c.4323_4328del NP_001341349.1:p.Pro1442_Pro1443del inframe deletion NM_001354429.2:c.4323_4328del NP_001341358.1:p.Pro1442_Pro1443del inframe deletion NC_000010.11:g.53827437_53827442del NC_000010.10:g.55587197_55587202del NG_009191.3:g.1806746_1806751del - Protein change
- Other names
- NM_001384140.1:c.4323_4328del
- Canonical SPDI
- NC_000010.11:53827431:GGCGGAGGCGG:GGCGG
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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
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
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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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PCDH15 | - | - |
GRCh38 GRCh37 |
3319 | 3406 |
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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Uncertain significance (1) |
criteria provided, single submitter
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Nov 1, 2022 | RCV003058249.2 | |
Uncertain significance (1) |
criteria provided, single submitter
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Jan 24, 2023 | RCV003062259.2 |
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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Uncertain significance
(Jan 24, 2023)
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criteria provided, single submitter
Method: curation
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Usher syndrome type 1F
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
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Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Accession: SCV003761035.1
First in ClinVar: Feb 07, 2023 Last updated: Feb 07, 2023 |
Comment:
The p.Pro1442_Pro1443del variant in PCDH15 has been reported in 1 individual individual with Usher syndrome type 1F (PMID: 16283880) and has been identified in 0.006% … (more)
The p.Pro1442_Pro1443del variant in PCDH15 has been reported in 1 individual individual with Usher syndrome type 1F (PMID: 16283880) and has been identified in 0.006% (1/15942) of African/African American chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs369289143). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. This variant is a duplication of 2 amino acids at position 1442 and is not predicted to alter the protein reading-frame. It is unclear if this deletion will impact the protein. In summary, the clinical significance of the p.Pro1442_Pro1443del variant is uncertain. ACMG/AMP Criteria applied: PM4_supporting, PM2_supporting (Richards 2015). (less)
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Uncertain significance
(Nov 01, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV003441430.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 14, 2024 |
Comment:
Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has … (more)
Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has been observed in individual(s) with clinical features of PCDH15-related conditions (PMID: 16283880). This variant is present in population databases (rs764861755, gnomAD 0.007%). This variant, c.4323_4328del, results in the deletion of 2 amino acid(s) of the PCDH15 protein (p.Pro1442_Pro1443del), but otherwise preserves the integrity of the reading frame. 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. (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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Assessment of the genetic causes of recessive childhood non-syndromic deafness in the UK - implications for genetic testing. | Hutchin T | Clinical genetics | 2005 | PMID: 16283880 |
Text-mined citations for this variant ...
HelpRecord last updated Mar 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.