Is CHST8 p.Gly62Ser (c.184G>A) pathogenic?

CHST8 p.Gly62Ser (c.184G>A) is classified Likely benign in CHST8 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-07). AlphaMissense: likely benign (0.0588); Very rare (popmax 0.00118%, sas).

How common is CHST8 p.Gly62Ser (c.184G>A) in the general population?

CHST8 p.Gly62Ser (c.184G>A) is very rare (popmax 0.00118%, sas) (gnomAD).

What do computational predictors say about CHST8 p.Gly62Ser (c.184G>A)?

AlphaMissense predicts likely benign (score 0.0588) — an in-silico prediction, not a clinical call.

CHST8 p.Gly62Ser

c.184G>A · VCV3492770

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0588 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00118%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0588	likely benign
REVEL	0.074	moderately benign-leaning
SaProt	LLR -5.66	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 -0.74	GERP -3.5
Regional constraint	o/e 1.04	unconstrained · MANE · 84 kb · p 0.3 · regional, not allelic
Overall
CADD	0.06	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 0.00118% South Asian · 1/84,884 alleles

Overall 0.000127% 2/1,570,612 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00118%	84,884
European (non-Finnish)	8.61e-05%	1,160,976

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: CHST8
Protein: p.Gly62Ser
Coding: c.184G>A
MANE Select: NM_001127895
Type: single nucleotide variant
Location: chr19:33771972 (GRCh38)
Gene constraint: LOEUF 1.001 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.90
Residue 62: the 'disordered' region

Full CHST8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHST8 p.Gly62Cys Uncertain significance ★ ⚠ same residue
CHST8 p.Val186Ala Uncertain significance ★★ ⚠ same type
CHST8 c.168+64G>A Benign ★★ same type
CHST8 c.-86-36C>T Benign ★★ same type
CHST8 p.Arg9= Benign ★★ same type
CHST8 p.Leu288= Benign ★★ same type
CHST8 p.Ala23Gly Uncertain significance ★ ⚠ same type
CHST8 p.Ala293Pro 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/chst8-p-gly62ser (accessed [today's date]).

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