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.512C>G (p.Pro171Arg)

CA213684

35999 (ClinVar)

Gene: DCLRE1C

Condition: severe combined immunodeficiency due to DCLRE1C deficiency

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: b82ebffe-f888-4104-91bf-516686f3b479

Approved on: 2024-01-17

Published on: 2024-01-17

HGVS expressions

NM_001033855.3:c.512C>G

NM_001033855.3(DCLRE1C):c.512C>G (p.Pro171Arg)

NC_000010.11:g.14934728G>C

CM000672.2:g.14934728G>C

NC_000010.10:g.14976727G>C

CM000672.1:g.14976727G>C

NC_000010.9:g.15016733G>C

NG_007276.1:g.24368C>G

ENST00000378278.7:c.512C>G

ENST00000357717.6:c.167C>G

ENST00000378241.5:c.152C>G

ENST00000378246.6:c.167C>G

ENST00000378249.5:c.167C>G

ENST00000378254.5:c.152C>G

ENST00000378255.5:c.152C>G

ENST00000378258.5:c.152C>G

ENST00000378278.6:c.512C>G

ENST00000378289.8:c.512C>G

ENST00000396817.6:c.152C>G

ENST00000418843.5:c.74C>G

ENST00000456122.1:c.167C>G

NM_001033855.2:c.512C>G

NM_001033857.2:c.152C>G

NM_001033858.2:c.152C>G

NM_001289076.1:c.167C>G

NM_001289077.1:c.152C>G

NM_001289078.1:c.167C>G

NM_001289079.1:c.152C>G

NM_022487.3:c.167C>G

NR_110297.1:n.1146C>G

NM_001350965.1:c.512C>G

NM_001350966.1:c.167C>G

NM_001350967.1:c.152C>G

NR_146960.1:n.934C>G

NR_146961.1:n.963C>G

NR_146962.1:n.934C>G

NM_001033857.3:c.152C>G

NM_001033858.3:c.152C>G

NM_001289076.2:c.167C>G

NM_001289077.2:c.152C>G

NM_001289078.2:c.167C>G

NM_001289079.2:c.152C>G

NM_001350965.2:c.512C>G

NM_001350966.2:c.167C>G

NM_001350967.2:c.152C>G

NM_022487.4:c.167C>G

NR_110297.2:n.810C>G

NR_146961.2:n.627C>G

Benign

BS2_Supporting BA1

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

The NM_001033855.3:c.512C>G variant in DCLRE1C is a missense variant predicted to cause the substitution of proline by arginine at amino acid 171 (p.Pro171Arg). This variant has an allele frequency of 0.19422 in the East Asian population in gnomAD, which is above the threshold for BA1 set by the ClinGen SCID VCEP for DCLRE1C (>0.00346). In addition, this variant is present 1394 adult homozygous individuals in gnomADv2.1.1 (distributed in all gnomAD populations)(BS2_Supporting). In summary, this variant meets the criteria to be classified as Benign for autosomal recessive SCID based on the ACMG criteria applied: BA1 and BS2_Supporting, as specified by the ClinGen SCID VCEP (VCEP specifications version 1).

BS2_Supporting

1394 adult homozygous individuals with this variant are present in gnomADv2.1.1 (distributed in all gnomAD populations)(BS2_Supporting).

BA1

In gnomAD, the overall minor allele frequency is 0.09068 (25647/282836 alleles) and the highest minor allele frequency (in East Asian population) is 0.19422 (3874/19946 alleles). This is greater than the allele frequency cutoff established by the ClinGen SCID VCEP for BA1 (>0.00346). In addition there are 1394 homozygotes in gnomAD for this variant. Therefore, BA1 criteria is met.

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