Is CDIN1 p.Arg187Pro (c.560G>C) pathogenic?

CDIN1 p.Arg187Pro (c.560G>C) is classified Uncertain significance in CDIN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-03). AlphaMissense: likely pathogenic (0.9982); Absent from gnomAD v4.1.

How common is CDIN1 p.Arg187Pro (c.560G>C) in the general population?

CDIN1 p.Arg187Pro (c.560G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDIN1 p.Arg187Pro (c.560G>C)?

AlphaMissense predicts likely pathogenic (score 0.9982) — an in-silico prediction, not a clinical call.

CDIN1 p.Arg187Pro

c.560G>C · rs1333441023 · VCV1962142

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9982 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9982	likely pathogenic · top 1% in CDIN1
REVEL	0.751	pathogenic-leaning
SaProt	LLR -17.03	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 229 kb · p 0.048 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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: CDIN1
Protein: p.Arg187Pro
Coding: c.560G>C
MANE Select: NM_001321759
dbSNP: rs1333441023
Type: single nucleotide variant
Location: chr15:36709238 (GRCh38)
Gene constraint: LOEUF 0.931 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.59

Full CDIN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDIN1 p.Ala100Ser Uncertain significance ★★ ⚠ same type
CDIN1 p.Arg101Trp Uncertain significance ★★ ⚠ same type
CDIN1 p.Glu66Ala Uncertain significance ★★ ⚠ same type
CDIN1 p.Pro33Leu Uncertain significance ★★ ⚠ same type
CDIN1 p.Thr271Lys Uncertain significance ★★ ⚠ same type
CDIN1 p.Tyr236Cys Uncertain significance ★★ ⚠ same type
CDIN1 p.Val203Phe Uncertain significance ★★ ⚠ same type
CDIN1 c.148-19G>T Benign/Likely 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/cdin1-p-arg187pro (accessed [today's date]).

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