Evidence Repository - Clinical Genome Resources

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.1284A>C (p.Lys428Asn)

CA5416508

287735 (ClinVar)

Gene: DCLRE1C

Condition: severe combined immunodeficiency due to DCLRE1C deficiency

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: a53b7359-07f9-40fc-b931-3c4d33611762

Approved on: 2024-02-05

Published on: 2024-02-05

HGVS expressions

NM_001033855.3:c.1284A>C

NM_001033855.3(DCLRE1C):c.1284A>C (p.Lys428Asn)

NC_000010.11:g.14909203T>G

CM000672.2:g.14909203T>G

NC_000010.10:g.14951202T>G

CM000672.1:g.14951202T>G

NC_000010.9:g.14991208T>G

NG_007276.1:g.49893A>C

ENST00000378278.7:c.1284A>C

ENST00000357717.6:c.939A>C

ENST00000378242.1:c.243A>C

ENST00000378246.6:c.939A>C

ENST00000378249.5:c.939A>C

ENST00000378254.5:c.924A>C

ENST00000378255.5:c.924A>C

ENST00000378258.5:c.924A>C

ENST00000378278.6:c.1284A>C

ENST00000378289.8:c.1157-9891A>C

ENST00000396817.6:c.924A>C

ENST00000489845.1:n.261A>C

ENST00000492201.5:n.499A>C

NM_001033855.2:c.1284A>C

NM_001033857.2:c.924A>C

NM_001033858.2:c.924A>C

NM_001289076.1:c.939A>C

NM_001289077.1:c.924A>C

NM_001289078.1:c.939A>C

NM_001289079.1:c.924A>C

NM_022487.3:c.939A>C

NR_110297.1:n.2059A>C

NM_001350965.1:c.1284A>C

NM_001350966.1:c.939A>C

NM_001350967.1:c.924A>C

NR_146960.1:n.1651A>C

NR_146961.1:n.1800A>C

NR_146962.1:n.1771A>C

NM_001033857.3:c.924A>C

NM_001033858.3:c.924A>C

NM_001289076.2:c.939A>C

NM_001289077.2:c.924A>C

NM_001289078.2:c.939A>C

NM_001289079.2:c.924A>C

NM_001350965.2:c.1284A>C

NM_001350966.2:c.939A>C

NM_001350967.2:c.924A>C

NM_022487.4:c.939A>C

NR_110297.2:n.1723A>C

NR_146961.2:n.1464A>C

Benign

BA1 BS2_Supporting

Evidence Links 0

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

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Severe Combined Immunodeficiency Disease VCEP

NM_001033855.3(DCLRE1C):c.1284A>C is a missense variant predicted to cause substitution of Lysine by Asparagine at amino acid 428 (p.Lys428Asn). The filtering allele frequency (the lower threshold of the 95% CI of 501/75018) of the c.1284A>C variant in DCLRE1C is 0.005719 for African/African American chromosomes by gnomAD v4, which is higher than the ClinGen SCID VCEP threshold (>0.00346) for BA1, and therefore meets this criterion (BA1). Additionally, 2 homozygous adults are reported in gnomAD v.4 in the same population. BS2_Supporting is Met. In summary, this variant meets the criteria to be classified as Benign for autosomal recessive severe combined immunodeficiency due to DCLRE1C deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID-VCEP: BA1 and BS2_Supporting. (VCEP specifications version 1).

BA1

The filtering allele frequency (the lower threshold of the 95% CI of 501/75018) of the c.1284A>C variant in DCLRE1C is 0.005719 for African/African American chromosomes by gnomAD v4, which is higher than the ClinGen SCID VCEP threshold (>0.00346) for BA1, and therefore meets this criterion (BA1).

BS2_Supporting

Additionally, 2 homozygous adults are reported in gnomAD v.4, in the same population. BS2_Supporting is Met.

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