Is CCDC78 p.Pro48= (c.144A>G) pathogenic?

CCDC78 p.Pro48= (c.144A>G) is classified Likely benign in CCDC78 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-01). Very rare (popmax 0.00488%, eas).

How common is CCDC78 p.Pro48= (c.144A>G) in the general population?

CCDC78 p.Pro48= (c.144A>G) is very rare (popmax 0.00488%, eas) (gnomAD).

CCDC78 p.Pro48=

c.144A>G · VCV4681890

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00488%, eas)

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 -2.2	GERP -3.2
Overall
CADD	0.927	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00488% East Asian · 2/41,004 alleles

Filtering AF 0.000808% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000302%

Overall 0.000143% 2/1,397,716 alleles · very rare

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: CCDC78
Protein: p.Pro48=
Coding: c.144A>G
MANE Select: NM_001378030
Type: single nucleotide variant
Location: chr16:726002 (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 c.1053+1G>A Uncertain significance ★★ same type
CCDC78 c.268-3C>T Uncertain significance ★★ same type
CCDC78 c.61-1G>A Uncertain significance ★★ same type
CCDC78 c.61-6C>A Uncertain significance ★★ same type
CCDC78 c.953+1G>A Uncertain significance ★★ same type
CCDC78 p.Ala126Val Uncertain significance ★★ ⚠ same type
CCDC78 p.Ala188Ser Uncertain significance ★★ ⚠ same type
CCDC78 p.Ala227Val 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-pro48 (accessed [today's date]).

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