Is CCDC120 p.Pro342Ser (c.1024C>T) pathogenic?

CCDC120 p.Pro342Ser (c.1024C>T) is classified Uncertain significance in CCDC120 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-26). AlphaMissense: likely pathogenic (0.9752); Absent from gnomAD v4.1.

How common is CCDC120 p.Pro342Ser (c.1024C>T) in the general population?

CCDC120 p.Pro342Ser (c.1024C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCDC120 p.Pro342Ser (c.1024C>T)?

AlphaMissense predicts likely pathogenic (score 0.9752) — an in-silico prediction, not a clinical call.

CCDC120 p.Pro342Ser

c.1024C>T · rs2064946787 · VCV3138297

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9752 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,169,270)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9752	likely pathogenic · top 3% in CCDC120
REVEL	0.283	benign-leaning
SaProt	LLR -8.33	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.6, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 4,747 bp · p 0.65 · regional, not allelic
Overall
CADD	25.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P307S vs ClinVar P342S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,169,270). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CCDC120
Protein: p.Pro342Ser
Coding: c.1024C>T
MANE Select: NM_001163321
dbSNP: rs2064946787
Type: single nucleotide variant
Location: chrX:49065808 (GRCh38)
Structure: AlphaFold pLDDT 56.34
Residue 342: the 'disordered' region

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

Similar variants

CCDC120 p.Pro342Leu Uncertain significance ★ ⚠ same residue
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

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-pro342ser (accessed [today's date]).

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