Is CDIN1 p.Ala38Pro (c.112G>C) pathogenic?

CDIN1 p.Ala38Pro (c.112G>C) is classified Conflicting classifications of pathogenicity in CDIN1 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-09-22). AlphaMissense: likely benign (0.2823); Rare (popmax 0.515%, eas).

How common is CDIN1 p.Ala38Pro (c.112G>C) in the general population?

CDIN1 p.Ala38Pro (c.112G>C) is rare (popmax 0.515%, eas) (gnomAD).

What do computational predictors say about CDIN1 p.Ala38Pro (c.112G>C)?

AlphaMissense predicts likely benign (score 0.2823) — an in-silico prediction, not a clinical call.

CDIN1 p.Ala38Pro

c.112G>C · rs182159142 · VCV1902444

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2823 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.515%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2823	likely benign
REVEL	0.154	moderately benign-leaning
SaProt	LLR -7.09	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 9.5	GERP 2.9, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 229 kb · p 0.048 · regional, not allelic
Overall
CADD	27.3	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.515% East Asian · 231/44,860 alleles

Filtering AF 0.46% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.439%

Overall 0.0147% 238/1,613,632 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.515%	194
Remaining individualsnot grpmax-eligible	0.008%	12,496
Admixed American	0.00167%	59,974
South Asian	0.0011%	91,032

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CDIN1
Protein: p.Ala38Pro
Coding: c.112G>C
MANE Select: NM_001321759
dbSNP: rs182159142
Type: single nucleotide variant
Location: chr15:36644288 (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-ala38pro (accessed [today's date]).

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