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Variant: NM_030621.4(DICER1):c.5125G>A (p.Asp1709Asn)

CA390865395

690480 (ClinVar)

Gene: DICER1 (HGNC:23405)
Condition: dicer1 syndrome (MONDO:0017288)
Inheritance Mode: Autosomal dominant inheritance
UUID: d7bb7946-aea7-4885-9715-4a46a61fd29f
Approved on: 2022-05-17
Published on: 2022-07-08

HGVS expressions

NM_030621.4(DICER1):c.5125G>A (p.Asp1709Asn)
NM_030621.4:c.5125G>A
NC_000014.9:g.95094127C>T
CM000676.2:g.95094127C>T
NC_000014.8:g.95560464C>T
CM000676.1:g.95560464C>T
NC_000014.7:g.94630217C>T
NG_016311.1:g.68296G>A
ENST00000343455.8:c.5125G>A
ENST00000393063.6:c.5125G>A
ENST00000526495.6:c.5125G>A
ENST00000556045.6:c.5125G>A
ENST00000675540.1:n.2870G>A
ENST00000675995.1:c.*3441G>A
ENST00000343455.7:c.5125G>A
ENST00000393063.5:c.5125G>A
ENST00000526495.5:c.5125G>A
ENST00000527414.5:c.5125G>A
ENST00000541352.5:c.5125G>A
ENST00000556045.5:c.1819G>A
NM_001195573.1:c.5125G>A
NM_001271282.2:c.5125G>A
NM_001291628.1:c.5125G>A
NM_177438.2:c.5125G>A
NM_001271282.3:c.5125G>A
NM_001291628.2:c.5125G>A
NM_177438.3:c.5125G>A
NM_001395677.1:c.5125G>A
NM_001395678.1:c.5125G>A
NM_001395679.1:c.5125G>A
NM_001395680.1:c.5125G>A
NM_001395682.1:c.5125G>A
NM_001395683.1:c.5125G>A
NM_001395684.1:c.5125G>A
NM_001395685.1:c.5125G>A
NM_001395686.1:c.4843G>A
NM_001395687.1:c.4720G>A
NM_001395688.1:c.4720G>A
NM_001395689.1:c.4720G>A
NM_001395690.1:c.4720G>A
NM_001395691.1:c.4558G>A
NM_001395697.1:c.3442G>A
NR_172715.1:n.5543G>A
NR_172716.1:n.5727G>A
NR_172717.1:n.5637G>A
NR_172718.1:n.5560G>A
NR_172719.1:n.5393G>A
NR_172720.1:n.5470G>A
NM_177438.3(DICER1):c.5125G>A (p.Asp1709Asn)
More

Pathogenic

Met criteria codes 6
PS2_Very Strong PS3_Supporting PM2_Supporting PM1 PS4_Moderate PP3
Not Met criteria codes 10
BS4 BS3 BS1 BP2 BP4 PM5 PS1 BA1 PP4 PP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen DICER1 and miRNA-Processing Gene Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DICER1 Version 1

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
DICER1 and miRNA-Processing Gene VCEP
The NM_177438.2:c.5125G>A variant in DICER1 is a missense variant predicted to cause substitution of aspartic acid by asparagine at amino acid 1709 (p.Asp1709Asn). This variant received a total of 2 phenotype points across 2 unrelated probands meeting DICER1 VCEP phenotype specificity scoring criteria of 2-3.5 points (PS4_Moderate, PMIDs: 26925222, 26475046). In both probands, this variant was identified as a de novo occurrence with constitutional mosaicism (PS2_Very Strong; PMIDs: 26925222, 26475046). This variant is absent from gnomAD v2.1.1 and v3.1.1 (non-cancer) (PM2_Supporting). In vitro cleavage assays in HEK293 cells showed that this variant fails to produce 5p microRNAs from a pre-miRNA, indicating that this variant impacts protein function (PS3_Supporting, PMIDs: 22187960, 26545620). The computational predictor REVEL gives a score of 0.868, which is above the threshold of 0.75, evidence that correlates with impact to DICER1 function (PP3). This variant resides in the p.D1709 metal ion-binding residue located in the RNase IIIb domain of DICER1, that is defined as a mutational hotspot and critical functional domain by the ClinGen DICER1 VCEP (PM1, PMID: 31342592). In summary, this variant meets the criteria to be classified as PATHOGENIC for DICER1 syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen DICER1 VCEP: PS4_Moderate, PS2_Very Strong, PM2_Supporting, PS3_Supporting, PP3, PM1. (Bayesian Points: 15; VCEP specifications version 1; 02/11/2022)
Met criteria codes
PS2_Very Strong
Confirmed de novo (constitutional mosaicism) in 2 probands with high-specificity phenotypes. (PMIDs: 26925222, 26475046)
PS3_Supporting
In vitro cleavage assays show impaired 5p cleavage (PMIDs: 22187960, 26545620)
PM2_Supporting
Allele is absent from gnomAD with >20x coverage in the region.
PM1
Putative missense variants affecting metal ion-binding residues (p.E1705, p.D1709, p.D1713, p.G1809, p.D1810, p.E1813)
PS4_Moderate
2 pts: 2 unrelated probands each with PPB and other DICER1-related phenotypes (PMIDs: 26925222, 26475046)
PP3
REVEL = 0.868 >0.75; no predicted splice impact
Not Met criteria codes
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
Multiple other variants in same codon but none are VCEP-curated yet and mostly somatic. ClinVar variation IDs: 933032, 933031, 933030, 932992, 690453, 477242, 932994, 932993
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
Code NA for germline variants in hotspot codons
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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