Is CDCA7 p.Gly245fs (c.734del) pathogenic?

CDCA7 p.Gly245fs (c.734del) is classified Uncertain significance in CDCA7 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-06-06). Very rare (popmax 8.48e-05%, nfe).

How common is CDCA7 p.Gly245fs (c.734del) in the general population?

CDCA7 p.Gly245fs (c.734del) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

CDCA7 p.Gly245fs

c.734del · rs2106391542 · VCV1373555

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

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 6 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.3	GERP 0.84, phastCons 0.98

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,178,784 alleles

Overall 6.86e-05% 1/1,458,232 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: CDCA7
Protein: p.Gly245fs
Coding: c.734del
MANE Select: NM_031942
dbSNP: rs2106391542
Type: Deletion
Location: chr2:173364827 (GRCh38)
Gene constraint: LOEUF 0.676 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.93 · 2 PDB

Full CDCA7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDCA7 p.Asn362fs Uncertain significance ★ same type
CDCA7 p.Lys18fs Uncertain significance ★ same type
CDCA7 p.Tyr438_Lys440delinsTer Uncertain significance ★ same type
CDCA7 c.1185+20del Likely benign ★ same type
CDCA7 c.1322+17_1322+19del Likely benign ★ same type
CDCA7 c.1322+19del Benign ★ same type
CDCA7 c.1323-12del Benign ★ same type
CDCA7 c.147+9del Likely benign ★ 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/cdca7-p-gly245fs (accessed [today's date]).

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