Is CBS p.Pro145Leu (c.434C>T) pathogenic?

CBS p.Pro145Leu (c.434C>T) is classified Pathogenic/Likely pathogenic in CBS (ClinVar, Multiple submitters, 8 submitters; last evaluated 2025-09-17). AlphaMissense: likely pathogenic (0.8847); Absent from gnomAD v4.1; Associated with homocystinuria.

What condition is associated with CBS p.Pro145Leu (c.434C>T)?

CBS p.Pro145Leu (c.434C>T) is associated with homocystinuria, classic homocystinuria (ClinVar).

How common is CBS p.Pro145Leu (c.434C>T) in the general population?

CBS p.Pro145Leu (c.434C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CBS p.Pro145Leu (c.434C>T)?

AlphaMissense predicts likely pathogenic (score 0.8847) — an in-silico prediction, not a clinical call.

CBS p.Pro145Leu

c.434C>T · rs121964963 · VCV118

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

AlphaMissense

likely pathogenic

0.8847 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,326,730)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

homocystinuria

Computational evidence

Protein change
AlphaMissense	0.8847	likely pathogenic ✓ concordant with ClinVar
REVEL	0.925	moderately pathogenic-leaning
SaProt	LLR -15.50	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.3, phastCons 1
Regional constraint	o/e 0.24	constrained · MANE · 1,046 bp · p 7.5e-10 · regional, not allelic
Overall
CADD	29.4	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

No allele count reported in gnomAD v4.1 (AN 1,326,730). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CBS
Protein: p.Pro145Leu
Coding: c.434C>T
MANE Select: NM_000071
dbSNP: rs121964963
Type: single nucleotide variant
Location: chr21:43066260 (GRCh38)
Structure: AlphaFold pLDDT 90.15 · 28 PDB
Residue 145: a β-strand; a UniProt-annotated variant site (in cbsd)

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

Disease context

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

Also linked: classic homocystinuria

Similar variants

CBS p.Pro145Arg Likely pathogenic ★ same residue
CBS p.Pro145= 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-pro145leu (accessed [today's date]).

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