ClinVar Genomic variation as it relates to human health
NM_001122630.2(CDKN1C):c.573GGCCCC[2] (p.186AP[8])
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
-
NM_001122630.2(CDKN1C):c.573GGCCCC[2] (p.186AP[8])
Variation ID: 236965 Accession: VCV000236965.40
- Type and length
-
Deletion, 12 bp
- Location
-
Cytogenetic: 11p15.4 11: 2884861-2884872 (GRCh38) [ NCBI UCSC ] 11: 2906091-2906102 (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 Oct 2, 2016 Oct 8, 2024 Aug 1, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_001122630.2:c.573GGCCCC[2] MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001116102.1:p.186AP[8] inframe deletion NM_000076.2:c.606GGCCCC[2] NP_000067.1:p.197AP[8] inframe deletion NM_000076.2:c.618_629del NM_000076.2:c.618_629delGGCCCCGGCCCC NM_001122631.2:c.573GGCCCC[2] NP_001116103.1:p.186AP[8] inframe deletion NM_001362474.2:c.606GGCCCC[2] NP_001349403.1:p.197AP[8] inframe deletion NM_001362475.2:c.255+318GGCCCC[2] intron variant NC_000011.10:g.2884866CGGGGC[2] NC_000011.9:g.2906096CGGGGC[2] NG_008022.1:g.5882GGCCCC[2] LRG_533:g.5882GGCCCC[2] LRG_533t1:c.606GGCCCC[2] LRG_533p1:p.197AP[8] - Protein change
- Other names
- -
- Canonical SPDI
- NC_000011.10:2884860:GGGGCCGGGGCCGGGGCCGGGGCCGGGGC:GGGGCCGGGGCCGGGGC
-
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.
-
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
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. |
|||
CDKN1C | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh38 GRCh37 |
1198 | 1233 |
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 (2) |
criteria provided, multiple submitters, no conflicts
|
Feb 1, 2024 | RCV000232076.14 | |
Benign (5) |
criteria provided, multiple submitters, no conflicts
|
Nov 10, 2017 | RCV000246892.15 | |
Benign/Likely benign (4) |
criteria provided, multiple submitters, no conflicts
|
Aug 1, 2024 | RCV001358515.24 |
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
(-)
|
criteria provided, single submitter
Method: clinical testing
|
NOT SPECIFIED
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics, part of Exact Sciences
Accession: SCV000301916.1
First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016 |
|
|
Benign
(Jul 31, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000333244.4
First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016 |
Number of individuals with the variant: 17
Sex: mixed
|
|
Likely benign
(Mar 16, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV001825822.1
First in ClinVar: Sep 08, 2021 Last updated: Sep 08, 2021 |
|
|
Benign
(Nov 10, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: no
Allele origin:
germline
|
Genetic Services Laboratory, University of Chicago
Accession: SCV002070467.1
First in ClinVar: Jan 29, 2022 Last updated: Jan 29, 2022 |
|
|
Benign
(Feb 24, 2020)
|
criteria provided, single submitter
Method: curation
|
Beckwith-Wiedemann syndrome
Affected status: unknown
Allele origin:
germline
|
Sema4, Sema4
Accession: SCV002534288.1
First in ClinVar: Jun 24, 2022 Last updated: Jun 24, 2022 |
|
|
Benign
(Feb 01, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Beckwith-Wiedemann syndrome
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000283420.10
First in ClinVar: Jul 01, 2016 Last updated: Feb 20, 2024 |
|
|
Benign
(Aug 01, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV002497100.17
First in ClinVar: Apr 08, 2022 Last updated: Oct 08, 2024 |
Comment:
CDKN1C: BS1, BS2
Number of individuals with the variant: 107
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
unknown
|
Department of Pathology and Laboratory Medicine, Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001554271.1 First in ClinVar: Apr 13, 2021 Last updated: Apr 13, 2021 |
Comment:
The CDKN1C p.Ala213_Pro216del variant was not identified in the literature nor was it identified in Cosmic. The variant was identified in dbSNP (ID: rs759134767), ClinVar … (more)
The CDKN1C p.Ala213_Pro216del variant was not identified in the literature nor was it identified in Cosmic. The variant was identified in dbSNP (ID: rs759134767), ClinVar (classified as benign by Invitae, Prevention Genetics and EGL Genetic Diagnostics) and LOVD 3.0. The variant was identified in control databases in 415 of 25528 chromosomes (6 homozygous) at a frequency of 0.016257 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 344 of 13620 chromosomes (freq: 0.02526), Ashkenazi Jewish in 6 of 258 chromosomes (freq: 0.02326), Latino in 6 of 416 chromosomes (freq: 0.01442), Other in 10 of 752 chromosomes (freq: 0.0133), European (Finnish) in 6 of 962 chromosomes (freq: 0.006237) and African in 43 of 7844 chromosomes (freq: 0.005482); it was not observed in the East Asian or South Asian populations. The variant occurs outside the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. This variant is an in-frame deletion resulting in the removal of the APAP residues between codons 213-216 in a non-conserved repeat region with unknown function. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. Therefore it is classified as likely benign. (less)
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001798063.1 First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021 |
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001931233.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001968360.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 2021 |
|
|
click to load more click to collapse |
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 |
---|---|---|---|---|
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CDKN1C | - | - | - | - |
Text-mined citations for rs759134767 ...
HelpRecord 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.