Is CHST6 p.Ile284Val (c.850A>G) pathogenic?

CHST6 p.Ile284Val (c.850A>G) is classified Uncertain significance in CHST6 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-15). AlphaMissense: likely benign (0.1627); Very rare (popmax 0.00223%, eas); Associated with Inborn genetic diseases.

What condition is associated with CHST6 p.Ile284Val (c.850A>G)?

CHST6 p.Ile284Val (c.850A>G) is associated with Inborn genetic diseases (ClinVar).

How common is CHST6 p.Ile284Val (c.850A>G) in the general population?

CHST6 p.Ile284Val (c.850A>G) is very rare (popmax 0.00223%, eas) (gnomAD).

What do computational predictors say about CHST6 p.Ile284Val (c.850A>G)?

AlphaMissense predicts likely benign (score 0.1627) — an in-silico prediction, not a clinical call.

CHST6 p.Ile284Val

c.850A>G · VCV3267245

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1627 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1627	likely benign
REVEL	0.391	indeterminate
SaProt	LLR -2.39	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.9	GERP 0.94, phastCons 1
Regional constraint	o/e 1.19	unconstrained · MANE · 1,184 bp · p 3.9e-06 · regional, not allelic
Overall
CADD	16.97	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 0.00223% East Asian · 1/44,870 alleles

Overall 6.85e-05% 1/1,460,542 alleles · very rare

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: CHST6
Protein: p.Ile284Val
Coding: c.850A>G
MANE Select: NM_021615
Type: single nucleotide variant
Location: chr16:75478979 (GRCh38)
Gene constraint: LOEUF 1.71 · pLI 0.26 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 90.66

Full CHST6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHST6 p.Ala286Val Uncertain significance ★★ ⚠ same condition
CHST6 p.Ala352Val Uncertain significance ★★ ⚠ same condition
CHST6 p.Arg240Ser Uncertain significance ★★ ⚠ same condition
CHST6 p.Arg267Cys Uncertain significance ★★ ⚠ same condition
CHST6 p.Arg344Cys Uncertain significance ★★ ⚠ same condition
CHST6 p.Gln82Pro Uncertain significance ★★ ⚠ same condition
CHST6 p.Glu317Gln Uncertain significance ★★ ⚠ same condition
CHST6 p.Gly238Asp Uncertain significance ★★ ⚠ 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/chst6-p-ile284val (accessed [today's date]).

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