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Variant: NM_001033855.3(DCLRE1C):c.247A>G (p.Ile83Val)

CA5416943

1515264 (ClinVar)

Gene: DCLRE1C
Condition: severe combined immunodeficiency due to DCLRE1C deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 8158ac9c-9dd2-42a1-aa93-a0407e9516b3
Approved on: 2024-02-15
Published on: 2024-02-15

HGVS expressions

NM_001033855.3:c.247A>G
NM_001033855.3(DCLRE1C):c.247A>G (p.Ile83Val)
NC_000010.11:g.14939869T>C
CM000672.2:g.14939869T>C
NC_000010.10:g.14981868T>C
CM000672.1:g.14981868T>C
NC_000010.9:g.15021874T>C
NG_007276.1:g.19227A>G
ENST00000378241.6:c.*294A>G
ENST00000456122.2:c.*489A>G
ENST00000489161.2:c.*81A>G
ENST00000492201.6:c.247A>G
ENST00000697047.1:c.247A>G
ENST00000697070.1:c.247A>G
ENST00000697071.1:c.*167A>G
ENST00000697072.1:c.247A>G
ENST00000697073.1:c.*81A>G
ENST00000697074.1:c.*81A>G
ENST00000697075.1:c.247A>G
ENST00000697076.1:c.247A>G
ENST00000697077.1:c.*14A>G
ENST00000697078.1:c.*13+2245A>G
ENST00000697079.1:n.67-4305A>G
ENST00000697080.1:c.*167A>G
ENST00000697081.1:c.247A>G
ENST00000697082.1:c.*489A>G
ENST00000697083.1:c.*167-3276A>G
ENST00000697084.1:c.247A>G
ENST00000697085.1:c.*14A>G
ENST00000697086.1:n.2684A>G
ENST00000697087.1:c.*167A>G
ENST00000697088.1:c.247A>G
ENST00000697089.1:c.*167A>G
ENST00000697090.1:n.255A>G
ENST00000697091.1:n.308A>G
ENST00000378278.7:c.247A>G
ENST00000357717.6:c.-43A>G
ENST00000378241.5:c.-114A>G
ENST00000378246.6:c.-43A>G
ENST00000378249.5:c.-43A>G
ENST00000378254.5:c.-114A>G
ENST00000378255.5:c.-114A>G
ENST00000378258.5:c.-114A>G
ENST00000378278.6:c.247A>G
ENST00000378289.8:c.247A>G
ENST00000396817.6:c.-114A>G
ENST00000418843.5:c.-151A>G
ENST00000456122.1:c.-43A>G
NM_001033855.2:c.247A>G
NM_001033857.2:c.-114A>G
NM_001033858.2:c.-114A>G
NM_001289076.1:c.-43A>G
NM_001289077.1:c.-114A>G
NM_001289078.1:c.-43A>G
NM_001289079.1:c.-114A>G
NM_022487.3:c.-43A>G
NR_110297.1:n.881A>G
NM_001350965.1:c.247A>G
NM_001350966.1:c.-43A>G
NM_001350967.1:c.-114A>G
NR_146960.1:n.669A>G
NR_146961.1:n.754A>G
NR_146962.1:n.669A>G
NM_001033857.3:c.-114A>G
NM_001033858.3:c.-114A>G
NM_001289076.2:c.-43A>G
NM_001289077.2:c.-114A>G
NM_001289078.2:c.-43A>G
NM_001289079.2:c.-114A>G
NM_001350965.2:c.247A>G
NM_001350966.2:c.-43A>G
NM_001350967.2:c.-114A>G
NM_022487.4:c.-43A>G
NR_110297.2:n.545A>G
NR_146961.2:n.418A>G

Uncertain Significance

Met criteria codes 1
PM2_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Severe Combined Immunodeficiency Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DCLRE1C Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Severe Combined Immunodeficiency Disease VCEP
The c.247A>G (NM_001033855.3) variant in DCLRE1C is a missense variant predicted to cause the substitution of Isoleucine by Valine at amino acid 83 (p.Ile83Val). The filtering allele frequency (the upper threshold of the 95% CI of 3/84132 alleles) of the c.247A>G variant in DCLRE1C is 0.000009470 for South Asian chromosomes by gnomAD v4, which is lower than the ClinGen SCID VCEP threshold (<0.00003266) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). No homozygotes have been observed in gnomAD. Another missense variant NM_001033855.3(DCLRE1C):c.247A>C (p.Ile83Leu) in the same codon has been reported; However, this variant was classified as VUS by the ClinGen SCID VCEP (PM5 not met). To our knowledge, this variant has not been reported in the literature in individuals affected with DCLRE1C-related conditions or in functional studies. In summary, this variant meets the criteria to be classified as a Variant of Uncertain Significance for autosomal recessive severe combined immunodeficiency due to DCLRE1C deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP: PM2_Supporting (VCEP specifications version 1).
Met criteria codes
PM2_Supporting
The filtering allele frequency (the upper threshold of the 95% CI of 3/84132 alleles) of the c.247A>G variant in DCLRE1C is 0.000009470 for South Asian chromosomes by gnomAD v4, which is lower than the ClinGen SCID VCEP threshold (<0.00003266) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). No homozygotes have been observed in gnomAD.
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