Is CCDC120 p.Asp201= (c.603T>C) pathogenic?

CCDC120 p.Asp201= (c.603T>C) is classified Likely benign in CCDC120 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-01). Absent from gnomAD v4.1.

How common is CCDC120 p.Asp201= (c.603T>C) in the general population?

CCDC120 p.Asp201= (c.603T>C) is absent from gnomAD v4.1 (gnomAD).

CCDC120 p.Asp201=

c.603T>C · rs2064929260 · VCV2660507

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 -2	GERP -2.1
Overall
CADD	4.842	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: CCDC120
Protein: p.Asp201=
Coding: c.603T>C
MANE Select: NM_001163321
dbSNP: rs2064929260
Type: single nucleotide variant
Location: chrX:49064543 (GRCh38)
Structure: AlphaFold pLDDT 56.34

Full CCDC120 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC120 c.63+12A>G Uncertain significance ★ same type
CCDC120 p.Ala126Thr Uncertain significance ★ ⚠ same type
CCDC120 p.Ala161Thr Uncertain significance ★ ⚠ same type
CCDC120 p.Ala164Gly Uncertain significance ★ ⚠ same type
CCDC120 p.Ala348Thr Uncertain significance ★ ⚠ same type
CCDC120 p.Ala376Val Uncertain significance ★ ⚠ same type
CCDC120 p.Ala405Thr Uncertain significance ★ ⚠ same type
CCDC120 p.Ala441Pro 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/ccdc120-p-asp201 (accessed [today's date]).

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