Is CBS p.His513Gln (c.1539C>G) pathogenic?

CBS p.His513Gln (c.1539C>G) is classified Uncertain significance in CBS (ClinVar, Single submitter, 1 submitter; last evaluated 2017-01-25). AlphaMissense: likely benign (0.2871); Absent from gnomAD v4.1.

How common is CBS p.His513Gln (c.1539C>G) in the general population?

CBS p.His513Gln (c.1539C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CBS p.His513Gln (c.1539C>G)?

AlphaMissense predicts likely benign (score 0.2871) — an in-silico prediction, not a clinical call.

CBS p.His513Gln

c.1539C>G · rs187828882 · VCV393133

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2871 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2871	likely benign
REVEL	0.667	pathogenic-leaning
SaProt	LLR -8.99	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.9	GERP -2.2
Regional constraint	o/e 0.00	constrained · MANE · 11 kb · p 6.7e-07 · regional, not allelic
Overall
CADD	6.576	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.His513Gln
Coding: c.1539C>G
MANE Select: NM_000071
dbSNP: rs187828882
Type: single nucleotide variant
Location: chr21:43056816 (GRCh38)
Structure: AlphaFold pLDDT 90.15 · 28 PDB
Residue 513: a β-strand

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

Similar variants

CBS p.His513= Conflicting classifications of pathogenicity ★ same residue
CBS p.His513Arg Uncertain significance ★ ⚠ same residue
CBS c.1145+1G>A Pathogenic/Likely pathogenic ★★ same type
CBS c.1223+1G>T Pathogenic ★★ same type
CBS c.1224-2A>C Pathogenic ★★ same type
CBS c.1358+1G>A Pathogenic ★★ same type
CBS c.1359-1G>C Pathogenic/Likely pathogenic ★★ same type
CBS c.1468-1G>A Likely pathogenic ★★ 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/cbs-p-his513gln (accessed [today's date]).

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