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NM_006904.7(PRKDC):c.8857A>T (p.Thr2953Ser)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Nov 2, 2021)
Last evaluated:
Dec 26, 2019
Accession:
VCV000475241.3
Variation ID:
475241
Description:
single nucleotide variant
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NM_006904.7(PRKDC):c.8857A>T (p.Thr2953Ser)

Allele ID
458945
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8q11.21
Genomic location
8: 47823923 (GRCh38) GRCh38 UCSC
8: 48736484 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_162:g.141261A>T
LRG_162t1:c.8857A>T LRG_162p1:p.Thr2953Ser
NM_006904.6:c.8857A>T NP_008835.5:p.Thr2953Ser missense
... more HGVS
Protein change
T2953S
Other names
-
Canonical SPDI
NC_000008.11:47823922:T:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00007
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00017
Trans-Omics for Precision Medicine (TOPMed) 0.00005
The Genome Aggregation Database (gnomAD), exomes 0.00010
The Genome Aggregation Database (gnomAD) 0.00006
Exome Aggregation Consortium (ExAC) 0.00010
Links
ClinGen: CA4739711
dbSNP: rs369402631
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Dec 26, 2019 RCV000549280.2
Uncertain significance 1 criteria provided, single submitter Sep 26, 2019 RCV001755901.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PRKDC - - GRCh38
GRCh37
929 981

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 26, 2019)
criteria provided, single submitter
Method: clinical testing
Immunodeficiency 26 with or without neurologic abnormalities
Allele origin: germline
Invitae
Accession: SCV000655401.2
Submitted: (Feb 06, 2020)
Evidence details
Comment:
This sequence change replaces threonine with serine at codon 2953 of the PRKDC protein (p.Thr2953Ser). The threonine residue is highly conserved and there is a … (more)
Uncertain significance
(Sep 26, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001995929.1
Submitted: (Nov 02, 2021)
Evidence details
Comment:
In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our … (more)

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs369402631...

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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