Is CHST11 p.Tyr331= (c.993C>T) pathogenic?

CHST11 p.Tyr331= (c.993C>T) is classified Likely benign in CHST11 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-24). Very rare (popmax 0.00167%, amr).

How common is CHST11 p.Tyr331= (c.993C>T) in the general population?

CHST11 p.Tyr331= (c.993C>T) is very rare (popmax 0.00167%, amr) (gnomAD).

CHST11 p.Tyr331=

c.993C>T · VCV4918211

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.11	GERP 0.079, phastCons 0.5
Overall
CADD	9.839	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,016 alleles

Filtering AF 0.000183% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00012%

Overall 0.000496% 8/1,614,064 alleles · very rare exomes 8/1,461,864 · genomes 0/152,200 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	60,016
Finnishnot grpmax-eligible	0.00156%	63,990
European (non-Finnish)	0.000508%	196,668

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: CHST11
Protein: p.Tyr331=
Coding: c.993C>T
MANE Select: NM_018413
Type: single nucleotide variant
Location: chr12:104757737 (GRCh38)
Gene constraint: LOEUF 0.511 · pLI 0.97 (gnomAD)
Structure: AlphaFold pLDDT 89.39

Full CHST11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHST11 p.Arg175His Uncertain significance ★★ ⚠ same type
CHST11 p.Ala224Pro Conflicting classifications of pathogenicity ★ ⚠ same type
CHST11 p.Ala94Thr Uncertain significance ★ ⚠ same type
CHST11 p.Arg10Lys Uncertain significance ★ ⚠ same type
CHST11 p.Arg219Cys Uncertain significance ★ ⚠ same type
CHST11 p.Arg42Gln Uncertain significance ★ ⚠ same type
CHST11 p.Arg42Trp Uncertain significance ★ ⚠ same type
CHST11 p.Arg53Gln 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/chst11-p-tyr331 (accessed [today's date]).

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