Is CHST9 p.Arg62Trp (c.184C>T) pathogenic?

CHST9 p.Arg62Trp (c.184C>T) is classified Uncertain significance in CHST9 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-13). AlphaMissense: likely benign (0.0749); Ultra-rare (popmax 0.0469%, eas).

How common is CHST9 p.Arg62Trp (c.184C>T) in the general population?

CHST9 p.Arg62Trp (c.184C>T) is ultra-rare (popmax 0.0469%, eas) (gnomAD).

What do computational predictors say about CHST9 p.Arg62Trp (c.184C>T)?

AlphaMissense predicts likely benign (score 0.0749) — an in-silico prediction, not a clinical call.

CHST9 p.Arg62Trp

c.184C>T · rs374613360 · VCV3144777

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0749 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0469%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0749	likely benign
REVEL	0.164	moderately benign-leaning
SaProt	LLR -8.46	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 1.2	GERP -4.8
Regional constraint	o/e 0.98	unconstrained · MANE · 227 kb · p 0.58 · regional, not allelic
Overall
CADD	16.91	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 0.0469% East Asian · 21/44,744 alleles

Filtering AF 0.0314% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0263%

Overall 0.0023% 37/1,611,572 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0469%	2,131
African / African-American	0.004%	24,969
Remaining individualsnot grpmax-eligible	0.0032%	31,212
Admixed American	0.00168%	59,640
Finnishnot grpmax-eligible	0.00156%	63,918
European (non-Finnish)	0.000763%	130,985

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: CHST9
Protein: p.Arg62Trp
Coding: c.184C>T
MANE Select: NM_031422
dbSNP: rs374613360
Type: single nucleotide variant
Location: chr18:27024134 (GRCh38)
Gene constraint: LOEUF 1.422 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.39

Full CHST9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHST9 p.Arg62Gln Likely benign ★ same residue
CHST9 p.Pro393= Benign ★★ same type
CHST9 p.Asn9Asp Uncertain significance ★ ⚠ same type
CHST9 p.Gly41Glu Uncertain significance ★ ⚠ same type
CHST9 p.Ile35Met Uncertain significance ★ ⚠ same type
CHST9 p.Lys72Arg Uncertain significance ★ ⚠ same type
CHST9 p.Met8Val Uncertain significance ★ ⚠ same type
CHST9 p.Pro57Leu 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/chst9-p-arg62trp (accessed [today's date]).

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