Is CIDEA p.Phe27Leu (c.79T>C) pathogenic?

CIDEA p.Phe27Leu (c.79T>C) is classified Likely benign in CIDEA (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-26). AlphaMissense: likely benign (0.1417); Absent from gnomAD v4.1.

How common is CIDEA p.Phe27Leu (c.79T>C) in the general population?

CIDEA p.Phe27Leu (c.79T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CIDEA p.Phe27Leu (c.79T>C)?

AlphaMissense predicts likely benign (score 0.1417) — an in-silico prediction, not a clinical call.

CIDEA p.Phe27Leu

c.79T>C · VCV3267348

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1417 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1417	likely benign
REVEL	0.029	moderately benign-leaning
SaProt	LLR -4.58	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 0.68	GERP -1.7, phastCons 0.22
Regional constraint	o/e 1.05	unconstrained · MANE · 23 kb · p 0.35 · regional, not allelic
Overall
CADD	6.161	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

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: CIDEA
Protein: p.Phe27Leu
Coding: c.79T>C
MANE Select: NM_001279
Type: single nucleotide variant
Location: chr18:12262865 (GRCh38)
Gene constraint: LOEUF 1.027 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.69 · 1 PDB

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

Similar variants

CIDEA p.Ala127Gly Uncertain significance ★ ⚠ same type
CIDEA p.Ala181Asp Uncertain significance ★ ⚠ same type
CIDEA p.Ala181Val Uncertain significance ★ ⚠ same type
CIDEA p.Arg128Thr Uncertain significance ★ ⚠ same type
CIDEA p.Arg162Trp Uncertain significance ★ ⚠ same type
CIDEA p.Arg175Gln Uncertain significance ★ ⚠ same type
CIDEA p.Arg175Trp Uncertain significance ★ ⚠ same type
CIDEA p.Arg197Gln 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/cidea-p-phe27leu (accessed [today's date]).

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