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NM_001080522.2(CC2D2A):c.2161C>T (p.Pro721Ser)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 25, 2020
Accession:
VCV000194821.6
Variation ID:
194821
Description:
single nucleotide variant
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NM_001080522.2(CC2D2A):c.2161C>T (p.Pro721Ser)

Allele ID
191984
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
4p15.32
Genomic location
4: 15540994 (GRCh38) GRCh38 UCSC
4: 15542617 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000004.11:g.15542617C>T
NC_000004.12:g.15540994C>T
NM_001080522.2:c.2161C>T NP_001073991.2:p.Pro721Ser missense
... more HGVS
Protein change
P721S
Other names
-
Canonical SPDI
NC_000004.12:15540993:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00399 (T)

Allele frequency
1000 Genomes Project 0.00399
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00035
The Genome Aggregation Database (gnomAD) 0.00061
Exome Aggregation Consortium (ExAC) 0.00527
Trans-Omics for Precision Medicine (TOPMed) 0.00081
Links
ClinGen: CA201373
UniProtKB: Q9P2K1#VAR_062804
dbSNP: rs199768782
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Jun 8, 2017 RCV000175282.2
Benign 1 criteria provided, single submitter Nov 25, 2020 RCV000860615.3
Benign 1 criteria provided, single submitter May 28, 2019 RCV000987417.1
Benign 1 criteria provided, single submitter Apr 27, 2017 RCV001147192.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CC2D2A - - GRCh38
GRCh37
799 845

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jun 08, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000612685.1
Submitted: (Aug 17, 2017)
Evidence details
Publications
PubMed (3)
Benign
(Mar 16, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000226748.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Joubert syndrome 1
Allele origin: unknown
Mendelics
Accession: SCV001136707.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Meckel syndrome type 6
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001307979.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Nov 25, 2020)
criteria provided, single submitter
Method: clinical testing
Joubert syndrome
Meckel-Gruber syndrome
Allele origin: germline
Invitae
Accession: SCV001000722.3
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
An informatics approach to analyzing the incidentalome. Berg JS Genetics in medicine : official journal of the American College of Medical Genetics 2013 PMID: 22995991
Mutation analysis of 18 nephronophthisis associated ciliopathy disease genes using a DNA pooling and next generation sequencing strategy. Otto EA Journal of medical genetics 2011 PMID: 21068128
CC2D2A mutations in Meckel and Joubert syndromes indicate a genotype-phenotype correlation. Mougou-Zerelli S Human mutation 2009 PMID: 19777577
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CC2D2A - - - -

Text-mined citations for rs199768782...

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These 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 Jun 14, 2021