Is DEPDC5 p.Ser930= (c.2790T>G) pathogenic?

DEPDC5 p.Ser930= (c.2790T>G) is classified Likely benign in DEPDC5 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-07-17). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DEPDC5 p.Ser930= (c.2790T>G)?

DEPDC5 p.Ser930= (c.2790T>G) is associated with Inborn genetic diseases (ClinVar).

How common is DEPDC5 p.Ser930= (c.2790T>G) in the general population?

DEPDC5 p.Ser930= (c.2790T>G) is absent from gnomAD v4.1 (gnomAD).

DEPDC5 p.Ser930=

c.2790T>G · rs2520124576 · VCV1796050

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

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 -4.9	GERP -8
Overall
CADD	1.51	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DEPDC5
Protein: p.Ser930=
Coding: c.2790T>G
MANE Select: NM_001242896
dbSNP: rs2520124576
Type: single nucleotide variant
Location: chr22:31843801 (GRCh38)
Gene constraint: LOEUF 0.403 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 65.22 · 11 PDB

Full DEPDC5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DEPDC5 c.1217+1G>A Likely pathogenic ★★ same condition
DEPDC5 p.Arg838Ter Pathogenic ★★ same condition
DEPDC5 c.2006+4A>G Uncertain significance ★★ same condition
DEPDC5 p.Ala1011Ser Uncertain significance ★★ ⚠ same condition
DEPDC5 p.Ala1091Val Uncertain significance ★★ ⚠ same condition
DEPDC5 p.Ala1287Thr Uncertain significance ★★ ⚠ same condition
DEPDC5 p.Ala1549Ser Uncertain significance ★★ ⚠ same condition
DEPDC5 p.Arg1001His 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/depdc5-p-ser930 (accessed [today's date]).

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