CDIN1 p.Phe240=
c.720T>C · VCV4691745
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00339%, nfe)
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 -1.4 | GERP -3.4 |
| Overall | ||
| CADD | 4.498 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00339%
European (non-Finnish) · 40/1,179,482 alleles
Filtering AF
0.00256%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00225%
Overall
0.0026%
42/1,613,252 alleles · very rare
exomes 39/1,461,110 · genomes 3/152,142 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00339% | 29,487 |
| Admixed American | 0.00167% | 59,968 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,428 |
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.Phe240=
- Coding
- c.720T>C
- MANE Select
- NM_001321759
- Type
- single nucleotide variant
- Location
- chr15:36808327 (GRCh38)
- Gene constraint
- LOEUF 0.931 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.59
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-phe240 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown