Is CYC1 p.Leu293Val (c.877T>G) pathogenic?

CYC1 p.Leu293Val (c.877T>G) is classified Uncertain significance in CYC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-24). AlphaMissense: likely benign (0.0895); Ultra-rare (popmax 0.0212%, nfe).

How common is CYC1 p.Leu293Val (c.877T>G) in the general population?

CYC1 p.Leu293Val (c.877T>G) is ultra-rare (popmax 0.0212%, nfe) (gnomAD).

What do computational predictors say about CYC1 p.Leu293Val (c.877T>G)?

AlphaMissense predicts likely benign (score 0.0895) — an in-silico prediction, not a clinical call.

CYC1 p.Leu293Val

c.877T>G · rs370734008 · VCV3079303

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0895 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0212%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0895	likely benign
REVEL	0.145	moderately benign-leaning
SaProt	LLR -8.77	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 -1.3	GERP -0.54, phastCons 0.001
Regional constraint	o/e 1.05	unconstrained · MANE · 2,233 bp · p 0.31 · regional, not allelic
Overall
CADD	7.037	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

Grpmax group 0.0212% European (non-Finnish) · 250/1,179,958 alleles

Filtering AF 0.019% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0182%

Overall 0.0159% 257/1,613,986 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0212%	4,720
Remaining individualsnot grpmax-eligible	0.008%	12,497
Admixed American	0.00167%	60,004
African / African-American	0.00133%	74,930

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: CYC1
Protein: p.Leu293Val
Coding: c.877T>G
MANE Select: NM_001916
dbSNP: rs370734008
Type: single nucleotide variant
Location: chr8:144097235 (GRCh38)
Gene constraint: LOEUF 0.583 · pLI 0.85 (gnomAD)
Structure: AlphaFold pLDDT 86.37 · 5 PDB
Residue 293: an α-helix

Full CYC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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CYC1 p.Arg285Gln Uncertain significance ★★ ⚠ same type
CYC1 p.Arg287His Uncertain significance ★★ ⚠ same type
CYC1 p.Arg308Gln Uncertain significance ★★ ⚠ same type
CYC1 p.Asn159Ser Uncertain significance ★★ ⚠ same type
CYC1 p.Asp173Asn Uncertain significance ★★ ⚠ same type
CYC1 p.Asp209Asn 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/cyc1-p-leu293val (accessed [today's date]).

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