The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_005026.5(PIK3CD):c.1642C>T (p.Arg548Trp)

CA577276

806050 (ClinVar)

Gene: PIK3CD (HGNC:5293)
Condition: immunodeficiency 14 (MONDO:0014222)
Inheritance Mode: Autosomal dominant inheritance
UUID: c6dcc9ff-882d-4aaa-972c-0d114fdabf56
Approved on: 2025-12-19
Published on: 2025-12-23

HGVS expressions

NM_005026.5:c.1642C>T
NM_005026.5(PIK3CD):c.1642C>T (p.Arg548Trp)
NC_000001.11:g.9720862C>T
CM000663.2:g.9720862C>T
NC_000001.10:g.9780920C>T
CM000663.1:g.9780920C>T
NC_000001.9:g.9703507C>T
NG_023434.1:g.74131C>T
ENST00000481137.2:c.*896C>T
ENST00000698709.1:c.1642C>T
ENST00000698710.1:c.1639C>T
ENST00000698712.1:c.1642C>T
ENST00000698713.1:c.1642C>T
ENST00000698714.1:c.1642C>T
ENST00000698715.1:c.1639C>T
ENST00000698716.1:c.1630C>T
ENST00000698718.1:n.712C>T
ENST00000698788.1:n.471C>T
ENST00000698789.1:c.318C>T
ENST00000377346.9:c.1642C>T
ENST00000361110.6:c.1714C>T
ENST00000377346.8:c.1642C>T
ENST00000536656.5:c.1714C>T
ENST00000543390.2:c.1714C>T
ENST00000628140.2:c.1714C>T
NM_005026.3:c.1642C>T
NM_001350234.1:c.1639C>T
NM_001350235.1:c.1555C>T
NM_005026.4:c.1642C>T
NM_001350234.2:c.1639C>T
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Uncertain Significance

Not Met criteria codes 7
BP4 PS4 PP4 PP3 PM2 PM5 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Antibody Deficiencies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PIK3CD Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Antibody Deficiencies VCEP
NM_005026.5(PIK3CD):c.1642C>T (p.Arg548Trp) is a missense variant causing substitution of arginine by tryptophan at amino acid 548. Another missense variant in the same codon, NM_005026.5(PIK3CD):c.1643G>A (p.Arg548Gln), has been reported in association with immunodeficiency 14 (SCV002301644.3) but has been classified as a VUS by the ClinGen Antibody Deficiencies VCEP, so PM5 is not met. This variant is present in gnomAD v4.1.0 at a total combined allele frequency of 0.00003730, with 60 alleles / 1,608,744 total alleles across all populations of gnomAD, which is higher than the ClinGen Antibody Deficiencies VCEP PM2_Supporting threshold of <0.00000132. The variant is present in gnomAD v.4.1.0 at a GrpMax allele frequency of 0.0001338, with 3 alleles / 6,074 total alleles in the Middle Eastern population, which is lower than the BS1 threshold of >0.000316, so no population code can be applied. This variant has been reported in 1 affected proband with a phenotype including recurrent fever, neurodevelopmental abnormalities (0.5 pts), and diarrhea (1 pt), which are not sufficient to meet the phenotype requirements for inclusion of the proband in PS4_Supporting (1.5 total points, ClinVar Accession #: SCV002524004.1). The computational predictor REVEL gives a score of 0.349, which is below the ClinGen Antibody Deficiencies VCEP threshold of >0.644 and does not predict a damaging effect on PIK3CD function. The computational predictor CADD gives a PHRED score of 29.0, which is above the ClinGen Antibody Deficiencies VCEP threshold of >25.3 and predicts a deleterious effect on PIK3CD function. Because the two predictors do not agree on a damaging effect, the PP3 code is not met. In summary, this variant meets the criteria to be classified as a variant of uncertain significance for autosomal dominant immunodeficiency 14 based on the ACMG/AMP criteria applied, as specified by the ClinGen Antibody Deficiencies VCEP: None. (VCEP specifications version 1.0.0).
Not Met criteria codes
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
This variant has been reported in 1 affected proband with a phenotype including recurrent fever, neurodevelopmental abnormalities (0.5 pts), and diarrhea (1 pt), which are not sufficient to meet the phenotype requirements for inclusion of the proband in PS4_Supporting (1.5 total points, ClinVar Accession #: SCV002524004.1).
PP4
Clinical Features: Recurrent fever (present) = 2 points (recurrent infection?) Neurodevelopmental abnormality (present) = 2 points (developmental delay?) Diarrhea (present) = 1 point (failure to thrive?) 5 PS4 points?
PP3
The computational predictor REVEL gives a score of 0.349, which is below the ClinGen Antibody Deficiencies VCEP threshold of >0.644 and does not predict a damaging effect on PIK3CD function. The computational predictor CADD gives a PHRED score of 29.0, which is above the ClinGen Antibody Deficiencies VCEP threshold of >25.3 and predicts a deleterious effect on PIK3CD function. Because the two predictors do not agree on a damaging effect, the PP3 code is not met.
PM2
This variant is present in gnomAD v4.1.0 at a total combined allele frequency of 0.00003730, with 60 alleles / 1,608,744 total alleles across all populations of gnomAD, which is higher than the ClinGen Antibody Deficiencies VCEP PM2_Supporting threshold of <0.00000132.
PM5
The NM_005026.5(PIK3CD):c.1643G>A (p.Arg548Gln) is classified as VUS by the Antibody VCEP rules.
BS1
This variant is present in gnomAD v.4.1.0 at a GrpMax allele frequency of 0.0001338, with 3 alleles / 6,074 total alleles in the Middle Eastern population, which is lower than the BS1 threshold of >0.000316, so no population code can be applied.
Curation History
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