Is DICER1 p.Arg790= (c.2370G>A) pathogenic?

DICER1 p.Arg790= (c.2370G>A) is classified Benign in DICER1 (ClinVar, Multiple submitters, 17 submitters; last evaluated 2026-04-16). Low-frequency (popmax 2.61%, afr); Associated with pleuropulmonary blastoma.

What condition is associated with DICER1 p.Arg790= (c.2370G>A)?

DICER1 p.Arg790= (c.2370G>A) is associated with pleuropulmonary blastoma, goiter, multinodular 1, with or without Sertoli-Leydig cell tumors, hereditary neoplastic syndrome (ClinVar).

How common is DICER1 p.Arg790= (c.2370G>A) in the general population?

DICER1 p.Arg790= (c.2370G>A) is low-frequency (popmax 2.61%, afr) (gnomAD).

How is Pleuropulmonary blastoma inherited?

Typically Autosomal dominant, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

DICER1 p.Arg790=

c.2370G>A · rs112712209 · VCV221128

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 17 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.61%, afr)

Conditions

pleuropulmonary blastoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.072	GERP -0.21, phastCons 0.9
Overall
CADD	9.628	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.61% African / African-American · 1,959/74,972 alleles

Filtering AF 2.52% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.48%

Overall 0.139% 2,243/1,614,012 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.61%	38
Remaining individualsnot grpmax-eligible	0.224%	446
Admixed American	0.172%	583
Middle Eastern	0.148%	674
South Asian	0.00769%	13,010
European (non-Finnish)	0.00212%	47,201

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DICER1
Protein: p.Arg790=
Coding: c.2370G>A
MANE Select: NM_177438
dbSNP: rs112712209
Type: single nucleotide variant
Location: chr14:95108390 (GRCh38)
Gene constraint: LOEUF 0.275 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 67.89 · 21 PDB
Residue 790: an α-helix

Full DICER1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

pleuropulmonary blastoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: goiter, multinodular 1, with or without Sertoli-Leydig cell tumors hereditary neoplastic syndrome global developmental delay - lung cysts - overgrowth - Wilms tumor syndrome DICER1-related tumor predisposition rhabdomyosarcoma, embryonal, 2

For Pleuropulmonary blastoma (Orphanet):

Inheritance: Autosomal dominant, Not applicable
Onset: Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

DICER1 p.Arg790Gln Uncertain significance ★ ⚠ same residue
DICER1 c.1509+16A>G Likely pathogenic ★★★ same condition
DICER1 c.1752+213A>G Likely pathogenic ★★★ same condition
DICER1 c.1753-9A>G Likely pathogenic ★★★ same condition
DICER1 c.1907+1G>A Pathogenic ★★★ same condition
DICER1 c.1908-3C>G Likely pathogenic ★★★ same condition
DICER1 c.2256+5G>A Likely pathogenic ★★★ same condition
DICER1 c.2256+5G>C Likely pathogenic ★★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dicer1-p-arg790 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown