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The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_001033855.3(DCLRE1C):c.350C>T (p.Pro117Leu)

CA5416895

522770 (ClinVar)

Gene: DCLRE1C
Condition: severe combined immunodeficiency due to DCLRE1C deficiency
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 186b5b74-1152-412c-bb7b-2d33fd28881b
Approved on: 2024-02-15
Published on: 2024-02-15

HGVS expressions

NM_001033855.3:c.350C>T
NM_001033855.3(DCLRE1C):c.350C>T (p.Pro117Leu)
NC_000010.11:g.14936550G>A
CM000672.2:g.14936550G>A
NC_000010.10:g.14978549G>A
CM000672.1:g.14978549G>A
NC_000010.9:g.15018555G>A
NG_007276.1:g.22546C>T
ENST00000378241.6:c.*397C>T
ENST00000456122.2:c.*549-986C>T
ENST00000489161.2:c.*141-986C>T
ENST00000492201.6:c.350C>T
ENST00000697047.1:c.350C>T
ENST00000697070.1:c.350C>T
ENST00000697071.1:c.*270C>T
ENST00000697072.1:c.350C>T
ENST00000697073.1:c.*141-986C>T
ENST00000697074.1:c.*141-986C>T
ENST00000697075.1:c.350C>T
ENST00000697076.1:c.350C>T
ENST00000697077.1:c.*74-986C>T
ENST00000697078.1:c.*57C>T
ENST00000697079.1:n.67-986C>T
ENST00000697080.1:c.*227-986C>T
ENST00000697081.1:c.307-986C>T
ENST00000697082.1:c.*549-986C>T
ENST00000697083.1:c.*210C>T
ENST00000697084.1:c.350C>T
ENST00000697085.1:c.*117C>T
ENST00000697086.1:n.2787C>T
ENST00000697087.1:c.*270C>T
ENST00000697088.1:c.307-986C>T
ENST00000697089.1:c.*270C>T
ENST00000697090.1:n.358C>T
ENST00000378278.7:c.350C>T
ENST00000357717.6:c.18-986C>T
ENST00000378241.5:c.-11C>T
ENST00000378246.6:c.18-986C>T
ENST00000378249.5:c.18-986C>T
ENST00000378254.5:c.-11C>T
ENST00000378255.5:c.-11C>T
ENST00000378258.5:c.-11C>T
ENST00000378278.6:c.350C>T
ENST00000378289.8:c.350C>T
ENST00000396817.6:c.-11C>T
ENST00000418843.5:c.-48C>T
ENST00000456122.1:c.18-986C>T
NM_001033855.2:c.350C>T
NM_001033857.2:c.-11C>T
NM_001033858.2:c.-11C>T
NM_001289076.1:c.18-986C>T
NM_001289077.1:c.-11C>T
NM_001289078.1:c.18-986C>T
NM_001289079.1:c.-11C>T
NM_022487.3:c.18-986C>T
NR_110297.1:n.984C>T
NM_001350965.1:c.350C>T
NM_001350966.1:c.18-986C>T
NM_001350967.1:c.-11C>T
NR_146960.1:n.772C>T
NR_146961.1:n.814-986C>T
NR_146962.1:n.772C>T
NM_001033857.3:c.-11C>T
NM_001033858.3:c.-11C>T
NM_001289076.2:c.18-986C>T
NM_001289077.2:c.-11C>T
NM_001289078.2:c.18-986C>T
NM_001289079.2:c.-11C>T
NM_001350965.2:c.350C>T
NM_001350966.2:c.18-986C>T
NM_001350967.2:c.-11C>T
NM_022487.4:c.18-986C>T
NR_110297.2:n.648C>T
NR_146961.2:n.478-986C>T

Uncertain Significance

Not Met criteria codes 1
PM2

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
NM_001033855.3(DCLRE1C):c.350C>T is a missense variant predicted to cause substitution of Proline by Leucine at amino acid 117 (p.Pro117Leu). The filtering allele frequency (the upper threshold of the 95% CI of 50/1178836) of the c.350C>T variant in DCLRE1C is 0.00003376 for European (non-Finnish) chromosomes by gnomAD v4, which is higher than the ClinGen SCID VCEP threshold (<0.00003266) for PM2_Supporting, and therefore do not meet this criterion. To our knowledge, this variant has not been reported in the literature in individuals affected with SCID/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 (specification version 1.0): No criteria were applied.
Not Met criteria codes
PM2
The filtering allele frequency (the upper threshold of the 95% CI of 50/1178836) of the c.350C>T variant in DCLRE1C is 0.00003376 for European (non-Finnish) chromosomes by gnomAD v4, which is higher than the ClinGen SCID VCEP threshold (<0.00003266) for PM2_Supporting, and therefore do not meet this criterion.
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