Is DRC2 c.1179+9del pathogenic?

DRC2 c.1179+9del is classified Likely benign in DRC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-25). Very rare (popmax 0.00837%, amr); Associated with primary ciliary dyskinesia 27.

What condition is associated with DRC2 c.1179+9del?

DRC2 c.1179+9del is associated with primary ciliary dyskinesia 27 (ClinVar).

How common is DRC2 c.1179+9del in the general population?

DRC2 c.1179+9del is very rare (popmax 0.00837%, amr) (gnomAD).

How is Primary ciliary dyskinesia inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DRC2 c.1179+9del

rs773082894 · VCV2723507

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00837%, amr)

Conditions

primary ciliary dyskinesia 27

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +9	near-intronic (+9 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.77	GERP 0.34
Overall
CADD	2.781	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00837% Admixed American · 5/59,744 alleles

Filtering AF 0.00324% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00287%

Overall 0.0036% 58/1,610,946 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00837%	11,949
European (non-Finnish)	0.00416%	24,038
Remaining individualsnot grpmax-eligible	0.00321%	31,164
African / African-American	0.00268%	37,381

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: DRC2
Coding: c.1179+9del
MANE Select: NM_033124
dbSNP: rs773082894
Type: Deletion
Location: chr12:48921089 (GRCh38)
Structure: AlphaFold pLDDT 83.21 · 1 PDB

Full DRC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia 27 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Primary ciliary dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Neonatal
Prevalence: 1-5 / 10 000 (Pakistan)

Similar variants

DRC2 p.Glu165fs Pathogenic ★★ same condition
DRC2 c.1026+8_1026+9del Benign/Likely benign ★★ same condition
DRC2 p.Asn232_Tyr233insTer Pathogenic ★ same condition
DRC2 p.Leu247fs Pathogenic ★ same condition
DRC2 p.Val302fs Pathogenic ★ same condition
DRC2 p.Val323fs Pathogenic ★ same condition
CCDC65 p.Phe457fs Uncertain significance ★ same condition
DRC2 p.Lys49_Ala55del Uncertain significance ★ 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/drc2-c-1179-plus-9del (accessed [today's date]).

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