Is CCDC65 p.Ser54= (c.162T>C) pathogenic?

CCDC65 p.Ser54= (c.162T>C) is classified Likely benign in CCDC65 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-08-02). Absent from gnomAD v4.1.

How common is CCDC65 p.Ser54= (c.162T>C) in the general population?

CCDC65 p.Ser54= (c.162T>C) is absent from gnomAD v4.1 (gnomAD).

CCDC65 p.Ser54=

c.162T>C · rs1592221032 · VCV762067

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -0.05	GERP -0.75, phastCons 0.88
Overall
CADD	8.308	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: CCDC65
Protein: p.Ser54=
Coding: c.162T>C
MANE Select: NM_033124
dbSNP: rs1592221032
Type: single nucleotide variant
Location: chr12:48904975 (GRCh38)
Gene constraint: LOEUF 1.004 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.21 · 1 PDB

Full CCDC65 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC65 p.Arg70Gln Uncertain significance ★★ ⚠ same type
CCDC65 p.Glu110Lys Uncertain significance ★★ ⚠ same type
CCDC65 p.Lys158Asn Uncertain significance ★★ ⚠ same type
DRC2 p.Ala109Val Uncertain significance ★★ ⚠ same type
DRC2 p.Ala114Pro Uncertain significance ★★ ⚠ same type
DRC2 p.Arg118Cys Uncertain significance ★★ ⚠ same type
DRC2 p.Arg294His Uncertain significance ★★ ⚠ same type
DRC2 p.Arg315Gln 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/ccdc65-p-ser54 (accessed [today's date]).

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