The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_177438.2(DICER1):c.4748T>G (p.Leu1583Arg)

CA212568

4468 (ClinVar)

Gene: DICER1
Condition: dicer1 syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: f699f55d-24ea-4c9b-882c-9ad1dc4b7531
Approved on: 2022-05-17
Published on: 2022-07-08

HGVS expressions

NM_177438.2:c.4748T>G
NM_177438.2(DICER1):c.4748T>G (p.Leu1583Arg)
NC_000014.9:g.95096172A>C
CM000676.2:g.95096172A>C
NC_000014.8:g.95562509A>C
CM000676.1:g.95562509A>C
NC_000014.7:g.94632262A>C
NG_016311.1:g.66251T>G
ENST00000343455.8:c.4748T>G
ENST00000393063.6:c.4748T>G
ENST00000526495.6:c.4748T>G
ENST00000532939.3:c.4748T>G
ENST00000556045.6:c.4748T>G
ENST00000675540.1:n.2493T>G
ENST00000675995.1:c.*3064T>G
ENST00000343455.7:c.4748T>G
ENST00000393063.5:c.4748T>G
ENST00000526495.5:c.4748T>G
ENST00000527414.5:c.4748T>G
ENST00000532939.2:n.783T>G
ENST00000541352.5:c.4748T>G
ENST00000556045.5:c.1442T>G
NM_001195573.1:c.4748T>G
NM_001271282.2:c.4748T>G
NM_001291628.1:c.4748T>G
NM_030621.4:c.4748T>G
NM_001271282.3:c.4748T>G
NM_001291628.2:c.4748T>G
NM_177438.3:c.4748T>G
NM_001395677.1:c.4748T>G
NM_001395678.1:c.4748T>G
NM_001395679.1:c.4748T>G
NM_001395680.1:c.4748T>G
NM_001395682.1:c.4748T>G
NM_001395683.1:c.4748T>G
NM_001395684.1:c.4748T>G
NM_001395685.1:c.4748T>G
NM_001395686.1:c.4466T>G
NM_001395687.1:c.4343T>G
NM_001395688.1:c.4343T>G
NM_001395689.1:c.4343T>G
NM_001395690.1:c.4343T>G
NM_001395691.1:c.4181T>G
NM_001395692.1:c.4748T>G
NM_001395693.1:c.4748T>G
NM_001395694.1:c.4748T>G
NM_001395695.1:c.4748T>G
NM_001395696.1:c.4343T>G
NM_001395697.1:c.3065T>G
NR_172715.1:n.5166T>G
NR_172716.1:n.5350T>G
NR_172717.1:n.5260T>G
NR_172718.1:n.5183T>G
NR_172719.1:n.5016T>G
NR_172720.1:n.5093T>G
NM_177438.3(DICER1):c.4748T>G (p.Leu1583Arg)

Likely Pathogenic

Met criteria codes 5
PS4_Supporting PM2_Supporting PP3 PP1_Moderate PS3_Supporting
Not Met criteria codes 12
BS4 BS3 BS1 BP2 BP4 BA1 PS2 PS1 PP4 PM6 PM1 PM5

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.4748T>G variant in DICER1 is a missense variant predicted to cause substitution of leucine by arginine at amino acid 1583 (p.Leu1583Arg). The variant has been reported to segregate with DICER1-related phenotypes in 3 affected family members from 1 family (PP1_moderate; PMID 19556464). This variant received a total of 1 phenotype point across 1 family meeting DICER1 VCEP phenotype specificity scoring criteria of 1-1.5 points (PS4_Supporting; PMID 19556464). 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 reduces the capacity of the protein to produce 5p/3p microRNAs from a pre-miRNA, indicating that this variant impacts protein function (Wu 2018, McGill University) (PS3_Supporting). The computational predictor REVEL gives a score of 0.894, which is above the threshold of 0.75, evidence that correlates with impact to DICER1 function (PP3). In summary, this variant meets the criteria to be classified as Likely pathogenic for DICER1 syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen DICER1 VCEP: PP1_moderate, PS4_supporting, PM2_supporting, PS3_supporting, PP3. (Bayesian Points: 6; VCEP specifications version 1; 02/11/2022)
Met criteria codes
PS4_Supporting
Reported as 4930T>G (L1573R) in 3 family members with DICER1-related phenotypes (PMID: 19556464).
PM2_Supporting
Absent gnomAD v.2.1.1 (non-cancer). Over 20x coverage in >90% individuals.
PP3
REVEL 0.894 >0.75; No splicing impact predicted by MaxEntScan and SpliceAI.
PP1_Moderate
Reported as 4930T>G (L1573R) in 3 family members with DICER1-related phenotypes (PMID: 19556464). (Proband with PPB; first cousin once removed with PPB; another first cousin once removed with lung cysts)
PS3_Supporting
Wu et al. 2018. PhD Thesis. "DICER1 syndrome: assays, associations and models" In vitro cleavage assay shows delayed 5p and 3p microRNAs from a pre-miRNA
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
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
NM_177438.2(DICER1):c.4747C>T (p.Leu1583Phe) - ClinVar Variation ID: 659266, VUS [Grantham Leu>Arg=102 > Leu>Phe=22]
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