Is CHST1 p.Arg363Ser (c.1087C>A) pathogenic?

CHST1 p.Arg363Ser (c.1087C>A) is classified Uncertain significance in CHST1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-15). AlphaMissense: ambiguous (0.3894); Absent from gnomAD v4.1.

How common is CHST1 p.Arg363Ser (c.1087C>A) in the general population?

CHST1 p.Arg363Ser (c.1087C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CHST1 p.Arg363Ser (c.1087C>A)?

AlphaMissense predicts ambiguous (score 0.3894) — an in-silico prediction, not a clinical call.

CHST1 p.Arg363Ser

c.1087C>A · VCV3267201

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3894 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,611,416)

Computational evidence

Protein change
AlphaMissense	0.3894	ambiguous
REVEL	0.378	indeterminate
SaProt	LLR -5.58	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.8	GERP -1.8, phastCons 1
Regional constraint	o/e 0.76	unconstrained · MANE · 1,232 bp · p 1.1e-08 · regional, not allelic
Overall
CADD	23.6	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 1,611,416). 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: CHST1
Protein: p.Arg363Ser
Coding: c.1087C>A
MANE Select: NM_003654
Type: single nucleotide variant
Location: chr11:45649837 (GRCh38)
Gene constraint: LOEUF 0.696 · pLI 0.14 (gnomAD)
Structure: AlphaFold pLDDT 87.90

Full CHST1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHST1 p.Arg59His Uncertain significance ★★ ⚠ same type
CHST1 p.Ala12Thr Uncertain significance ★ ⚠ same type
CHST1 p.Ala388Thr Uncertain significance ★ ⚠ same type
CHST1 p.Ala43Val Uncertain significance ★ ⚠ same type
CHST1 p.Ala54Thr Uncertain significance ★ ⚠ same type
CHST1 p.Arg114Gln Uncertain significance ★ ⚠ same type
CHST1 p.Arg198Ser Uncertain significance ★ ⚠ same type
CHST1 p.Arg217His 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/chst1-p-arg363ser (accessed [today's date]).

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