Is CBS p.Ser466Leu (c.1397C>T) pathogenic?

CBS p.Ser466Leu (c.1397C>T) is classified Conflicting classifications of pathogenicity in CBS (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2024-11-11). AlphaMissense: likely benign (0.1763); Absent from gnomAD v4.1; Associated with classic homocystinuria.

What condition is associated with CBS p.Ser466Leu (c.1397C>T)?

CBS p.Ser466Leu (c.1397C>T) is associated with classic homocystinuria, familial thoracic aortic aneurysm and aortic dissection (ClinVar).

How common is CBS p.Ser466Leu (c.1397C>T) in the general population?

CBS p.Ser466Leu (c.1397C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CBS p.Ser466Leu (c.1397C>T)?

AlphaMissense predicts likely benign (score 0.1763) — an in-silico prediction, not a clinical call.

CBS p.Ser466Leu

Q: How is Homocystinuria due to cystathionine beta-synthase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.1397C>T · rs121964971 · VCV130

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

AlphaMissense

likely benign

0.1763 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

classic homocystinuria

Computational evidence

Protein change
AlphaMissense	0.1763	likely benign
REVEL	0.822	moderately pathogenic-leaning
SaProt	LLR -12.46	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.2	GERP 0.17, phastCons 1
Regional constraint	o/e 0.00	constrained · MANE · 11 kb · p 6.7e-07 · regional, not allelic
Overall
CADD	25.5	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: CBS
Protein: p.Ser466Leu
Coding: c.1397C>T
MANE Select: NM_000071
dbSNP: rs121964971
Type: single nucleotide variant
Location: chr21:43058215 (GRCh38)
Structure: AlphaFold pLDDT 90.15 · 28 PDB
Residue 466: the cbs domain; a UniProt-annotated variant site (in cbsd; increased cystathionine beta-synthase activity; impaired stimulation by adomet and adohcy; decreased homotetramer formation); an α-helix

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

Disease context

classic homocystinuria — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: familial thoracic aortic aneurysm and aortic dissection

For Homocystinuria due to cystathionine beta-synthase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood
Prevalence: 1-9 / 1 000 000 (Worldwide)

Similar variants

CBS p.Ser466Ter Pathogenic ★★ same residue
CBS p.Ser466= Likely benign ★★ same residue
CBS c.1145+1G>A Pathogenic/Likely pathogenic ★★ same condition
CBS c.1223+1G>T Pathogenic ★★ same condition
CBS c.1224-2A>C Pathogenic ★★ same condition
CBS c.1358+1G>A Pathogenic ★★ same condition
CBS c.1359-1G>C Pathogenic/Likely pathogenic ★★ same condition
CBS c.1468-1G>A Likely pathogenic ★★ same condition

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/cbs-p-ser466leu (accessed [today's date]).

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