Variant: NM_001033855.3(DCLRE1C):c.457G>T (p.Gly153Trp)

CA5416841

879949 (ClinVar)

Gene: DCLRE1C

Condition: severe combined immunodeficiency due to DCLRE1C deficiency

Inheritance Mode: Autosomal recessive inheritance

UUID: f009a83a-a535-423d-9b35-49736113d10e

Approved on: 2024-06-13

Published on: 2024-06-13

HGVS expressions

NM_001033855.3:c.457G>T
NM_001033855.3(DCLRE1C):c.457G>T (p.Gly153Trp)
NC_000010.11:g.14935470C>A
CM000672.2:g.14935470C>A
NC_000010.10:g.14977469C>A
CM000672.1:g.14977469C>A
NC_000010.9:g.15017475C>A
NG_007276.1:g.23626G>T
ENST00000378241.6:c.*504G>T
ENST00000456122.2:c.*643G>T
ENST00000489161.2:c.*235G>T
ENST00000492201.6:c.457G>T
ENST00000697047.1:c.457G>T
ENST00000697070.1:c.457G>T
ENST00000697071.1:c.*377G>T
ENST00000697072.1:c.457G>T
ENST00000697073.1:c.*235G>T
ENST00000697074.1:c.*235G>T
ENST00000697075.1:c.457G>T
ENST00000697076.1:c.457G>T
ENST00000697077.1:c.*168G>T
ENST00000697078.1:c.*164G>T
ENST00000697079.1:n.161G>T
ENST00000697080.1:c.*321G>T
ENST00000697081.1:c.*74G>T
ENST00000697082.1:c.*643G>T
ENST00000697083.1:c.*317G>T
ENST00000697084.1:c.457G>T
ENST00000697085.1:c.*224G>T
ENST00000697086.1:n.2894G>T
ENST00000697087.1:c.*377G>T
ENST00000697088.1:c.*74G>T
ENST00000697089.1:c.*377G>T
ENST00000697090.1:n.465G>T
ENST00000378278.7:c.457G>T
ENST00000357717.6:c.112G>T
ENST00000378241.5:c.97G>T
ENST00000378246.6:c.112G>T
ENST00000378249.5:c.112G>T
ENST00000378254.5:c.97G>T
ENST00000378255.5:c.97G>T
ENST00000378258.5:c.97G>T
ENST00000378278.6:c.457G>T
ENST00000378289.8:c.457G>T
ENST00000396817.6:c.97G>T
ENST00000418843.5:c.19G>T
ENST00000456122.1:c.112G>T
NM_001033855.2:c.457G>T
NM_001033857.2:c.97G>T
NM_001033858.2:c.97G>T
NM_001289076.1:c.112G>T
NM_001289077.1:c.97G>T
NM_001289078.1:c.112G>T
NM_001289079.1:c.97G>T
NM_022487.3:c.112G>T
NR_110297.1:n.1091G>T
NM_001350965.1:c.457G>T
NM_001350966.1:c.112G>T
NM_001350967.1:c.97G>T
NR_146960.1:n.879G>T
NR_146961.1:n.908G>T
NR_146962.1:n.879G>T
NM_001033857.3:c.97G>T
NM_001033858.3:c.97G>T
NM_001289076.2:c.112G>T
NM_001289077.2:c.97G>T
NM_001289078.2:c.112G>T
NM_001289079.2:c.97G>T
NM_001350965.2:c.457G>T
NM_001350966.2:c.112G>T
NM_001350967.2:c.97G>T
NM_022487.4:c.112G>T
NR_110297.2:n.755G>T
NR_146961.2:n.572G>T

Uncertain Significance

• Met criteria codes: PM2_Supporting

• Not Met criteria codes: BS2

Expert Panel

Severe Combined Immunodeficiency Disease VCEP

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

Evidence submitted by expert panel

Severe Combined Immunodeficiency Disease VCEP

The c.457G>T (NM_001033855.3) variant in DCLRE1C is a missense variant predicted to cause substitution of Glycine by Tryptophan at amino acid 153 (p.Gly153Trp). The filtering allele frequency (the upper threshold of the 95% CI of 8/1111862 alleles) of the c.457G>T variant in DCLRE1C is 0.000003100 for European (non-Finnish) 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. 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: PM2_Supporting (VCEP specifications version 1).

Met criteria codes

• PM2_Supporting: The filtering allele frequency (the upper threshold of the 95% CI of 8/1111862 alleles) of the c.457G>T variant in DCLRE1C is 0.000003100 for European (non-Finnish) 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.

Not Met criteria codes

• BS2: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline