Is CCDC78 p.Arg282fs (c.844del) pathogenic?

CCDC78 p.Arg282fs (c.844del) is classified Uncertain significance in CCDC78 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-09-01). Absent from gnomAD.

How common is CCDC78 p.Arg282fs (c.844del) in the general population?

CCDC78 p.Arg282fs (c.844del) is absent from gnomAD (gnomAD).

CCDC78 p.Arg282fs

c.844del · rs1567318347 · VCV623880

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 9 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.1	GERP -0.38, phastCons 0.002

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CCDC78
Protein: p.Arg282fs
Coding: c.844del
MANE Select: NM_001378030
dbSNP: rs1567318347
Type: Deletion
Location: chr16:724431 (GRCh38)
Gene constraint: LOEUF 1.615 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.65

Full CCDC78 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC78 p.Arg282Gln Uncertain significance ★★ ⚠ same residue
CCDC78 p.Arg282Gly Uncertain significance ★★ ⚠ same residue
CCDC78 p.Arg282Trp Uncertain significance ★★ ⚠ same residue
CCDC78 p.Arg282= Likely benign ★ same residue
CCDC78 p.Gln371fs Uncertain significance ★★ same type
CCDC78 p.Leu292fs Uncertain significance ★★ same type
CCDC78 c.1134-131del Benign ★★ same type
CCDC78 c.1200+14_1200+18del Uncertain significance ★ same type

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/ccdc78-p-arg282fs (accessed [today's date]).

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