Is CCDC174 p.Pro446Arg (c.1337C>G) pathogenic?

CCDC174 p.Pro446Arg (c.1337C>G) is classified Uncertain significance in CCDC174 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-14). AlphaMissense: likely benign (0.0723); Absent from gnomAD v4.1.

How common is CCDC174 p.Pro446Arg (c.1337C>G) in the general population?

CCDC174 p.Pro446Arg (c.1337C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCDC174 p.Pro446Arg (c.1337C>G)?

AlphaMissense predicts likely benign (score 0.0723) — an in-silico prediction, not a clinical call.

CCDC174 p.Pro446Arg

c.1337C>G · VCV3996744

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0723 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0723	likely benign
REVEL	0.058	moderately benign-leaning
SaProt	LLR -7.96	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.2	GERP 1.6, phastCons 0.01
Regional constraint	o/e 0.94	unconstrained · MANE · 19 kb · p 0.15 · regional, not allelic
Overall
CADD	15.64	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

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: CCDC174
Protein: p.Pro446Arg
Coding: c.1337C>G
MANE Select: NM_016474
Type: single nucleotide variant
Location: chr3:14671127 (GRCh38)
Gene constraint: LOEUF 0.926 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.79
Residue 446: the 'disordered' region

Full CCDC174 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC174 p.Asp395His Uncertain significance ★★ ⚠ same type
CCDC174 p.Phe29Ser Uncertain significance ★★ ⚠ same type
CCDC174 p.Pro158Ser Uncertain significance ★★ ⚠ same type
CCDC174 c.1106-10T>A Benign/Likely benign ★★ same type
CCDC174 c.308-55C>A Benign ★★ same type
CCDC174 c.485+47G>A Benign ★★ same type
CCDC174 c.485+83C>G Benign ★★ same type
CCDC174 c.485+83C>T 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/ccdc174-p-pro446arg (accessed [today's date]).

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