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NM_001195263.2(PDZD7):c.2144C>T (p.Pro715Leu)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Sep 23, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000044123.8
Variation ID:
44123
Description:
single nucleotide variant
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NM_001195263.2(PDZD7):c.2144C>T (p.Pro715Leu)

Allele ID
53291
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q24.31
Genomic location
10: 101010745 (GRCh38) GRCh38 UCSC
10: 102770502 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.102770502G>A
NC_000010.11:g.101010745G>A
NG_028030.1:g.25413C>T
NM_001195263.2:c.2144C>T MANE Select NP_001182192.1:p.Pro715Leu missense
Protein change
P715L
Other names
-
Canonical SPDI
NC_000010.11:101010744:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00599 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00712
The Genome Aggregation Database (gnomAD) 0.00754
Exome Aggregation Consortium (ExAC) 0.00658
The Genome Aggregation Database (gnomAD), exomes 0.00750
Trans-Omics for Precision Medicine (TOPMed) 0.00798
1000 Genomes Project 0.00599
Links
ClinGen: CA133625
dbSNP: rs143414291
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Jan 25, 2018 RCV000037099.5
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000954274.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PDZD7 - - GRCh38
GRCh37
417 431

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Nov 20, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001908869.1
Submitted: (Sep 21, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 24498627)
Benign
(Jan 25, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000060756.6
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Pro715Leu in exon 15 of PDZD7: This variant is not expected to have clinical s ignificance because it has been identified in 4.3% (10/230) of … (more)
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001100897.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jan 23, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000226253.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
http://www.ncbi.nlm.nih.gov/vari…
Likely benign
(Aug 31, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001144893.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (1)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001923342.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
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: SCV001972498.1
Submitted: (Sep 21, 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
Experience of targeted Usher exome sequencing as a clinical test. Besnard T Molecular genetics & genomic medicine 2014 PMID: 24498627
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PDZD7 - - - -
http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/?chr=10&from=102770502&to=102770502 - - - -

Text-mined citations for rs143414291...

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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 Nov 27, 2021