NM_006904.7(PRKDC):c.5572-4G>A AND Immunodeficiency 26 with or without neurologic abnormalities

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: Oct 7, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000768056.3

Allele description [Variation Report for NM_006904.7(PRKDC):c.5572-4G>A]

NM_006904.7(PRKDC):c.5572-4G>A

Gene:
PRKDC:protein kinase, DNA-activated, catalytic subunit [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8q11.21
Genomic location:
Preferred name:
NM_006904.7(PRKDC):c.5572-4G>A
HGVS:
  • NC_000008.11:g.47863581C>T
  • NG_023435.1:g.101603G>A
  • NM_001081640.2:c.5572-4G>A
  • NM_006904.6:c.5572-4G>A
  • NM_006904.7:c.5572-4G>AMANE SELECT
  • LRG_162t1:c.5572-4G>A
  • LRG_162:g.101603G>A
  • NC_000008.10:g.48776142C>T
Links:
dbSNP: rs367584015
NCBI 1000 Genomes Browser:
rs367584015
Molecular consequence:
  • NM_001081640.2:c.5572-4G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_006904.6:c.5572-4G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_006904.7:c.5572-4G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Immunodeficiency 26 with or without neurologic abnormalities (IMD26)
Synonyms:
IMMUNODEFICIENCY 26 WITH NEUROLOGIC ABNORMALITIES
Identifiers:
MONDO: MONDO:0014423; MedGen: C4014833; OMIM: 615966

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000898910Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicagocriteria provided, single submitter
Uncertain significance
(Nov 30, 2018)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001039436Invitaecriteria provided, single submitter
Likely benign
(Oct 7, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV000898910.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

PRKDC NM_006904.6 exon 42 c.5571-4G>A: This variant has not been reported in the literature and is present in 0.07% (25/33386) of Latino alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/8-48776142-C-T). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. Although this variant occurs in the splice region, computational prediction tools do not suggest that it may alter splicing. However, further studies are needed to understand its impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001039436.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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