Is CHST7 p.Pro182Arg (c.545C>G) pathogenic?

CHST7 p.Pro182Arg (c.545C>G) is classified Uncertain significance in CHST7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-21). AlphaMissense: likely benign (0.0769); Ultra-rare (popmax 0.0124%, nfe).

How common is CHST7 p.Pro182Arg (c.545C>G) in the general population?

CHST7 p.Pro182Arg (c.545C>G) is ultra-rare (popmax 0.0124%, nfe) (gnomAD).

What do computational predictors say about CHST7 p.Pro182Arg (c.545C>G)?

AlphaMissense predicts likely benign (score 0.0769) — an in-silico prediction, not a clinical call.

CHST7 p.Pro182Arg

c.545C>G · VCV3833284

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0769 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0124%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.0769	likely benign
REVEL	0.422	indeterminate
SaProt	LLR -6.48	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 -0.12	GERP 1.1
Regional constraint	o/e 0.73	unconstrained · MANE · 1,017 bp · p 1.6e-06 · regional, not allelic
Overall
CADD	21.1	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 0.0124% European (non-Finnish) · 111/892,823 alleles

Filtering AF 0.0106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00983%

Overall 0.00954% 115/1,205,389 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0124%	8,043
Finnishnot grpmax-eligible	0.00442%	22,641
Remaining individualsnot grpmax-eligible	0.00422%	23,679

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: CHST7
Protein: p.Pro182Arg
Coding: c.545C>G
MANE Select: NM_019886
Type: single nucleotide variant
Location: chrX:46574476 (GRCh38)
Structure: AlphaFold pLDDT 80.60

Full CHST7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHST7 p.Asp266= Benign ★★ same type
CHST7 p.Ala172Thr Uncertain significance ★ ⚠ same type
CHST7 p.Ala337Thr Uncertain significance ★ ⚠ same type
CHST7 p.Ala413Ser Uncertain significance ★ ⚠ same type
CHST7 p.Ala413Thr Uncertain significance ★ ⚠ same type
CHST7 p.Ala453Val Uncertain significance ★ ⚠ same type
CHST7 p.Arg323Cys Uncertain significance ★ ⚠ same type
CHST7 p.Arg354Ser 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/chst7-p-pro182arg (accessed [today's date]).

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