Is CHST2 p.Asn87Ser (c.260A>G) pathogenic?

CHST2 p.Asn87Ser (c.260A>G) is classified Likely benign in CHST2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-01). AlphaMissense: likely benign (0.0659); Rare (popmax 0.21%, mid).

How common is CHST2 p.Asn87Ser (c.260A>G) in the general population?

CHST2 p.Asn87Ser (c.260A>G) is rare (popmax 0.21%, mid) (gnomAD).

What do computational predictors say about CHST2 p.Asn87Ser (c.260A>G)?

AlphaMissense predicts likely benign (score 0.0659) — an in-silico prediction, not a clinical call.

CHST2 p.Asn87Ser

c.260A>G · rs374335239 · VCV2383427

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0659 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.21%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0659	likely benign
REVEL	0.193	benign-leaning
SaProt	LLR -3.64	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	phastCons 1
Regional constraint	o/e 1.18	unconstrained · MANE · 481 bp · p 0.0045 · regional, not allelic
Overall
CADD	14.43	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

Grpmax group 0.21% Middle Eastern · 9/4,276 alleles

Filtering AF 0.11% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.082%

Overall 0.00881% 133/1,510,310 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.21%	475
African / African-American	0.0929%	1,076
Admixed American	0.0306%	3,269
Remaining individualsnot grpmax-eligible	0.0275%	3,637
South Asian	0.00376%	26,573
European (non-Finnish)	0.00238%	41,932

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: CHST2
Protein: p.Asn87Ser
Coding: c.260A>G
MANE Select: NM_004267
dbSNP: rs374335239
Type: single nucleotide variant
Location: chr3:143121076 (GRCh38)
Gene constraint: LOEUF 1.15 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.61

Full CHST2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHST2 p.Ala116Pro Uncertain significance ★ ⚠ same type
CHST2 p.Ala116Ser Uncertain significance ★ ⚠ same type
CHST2 p.Ala118Gly Uncertain significance ★ ⚠ same type
CHST2 p.Ala131Val Uncertain significance ★ ⚠ same type
CHST2 p.Ala24Val Uncertain significance ★ ⚠ same type
CHST2 p.Ala25Thr Uncertain significance ★ ⚠ same type
CHST2 p.Ala387Gly Uncertain significance ★ ⚠ same type
CHST2 p.Ala455Val 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/chst2-p-asn87ser (accessed [today's date]).

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