Is CHST7 p.Pro335Thr (c.1003C>A) pathogenic?

CHST7 p.Pro335Thr (c.1003C>A) is classified Uncertain significance in CHST7 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-11). AlphaMissense: likely benign (0.0989); Absent from gnomAD v4.1.

How common is CHST7 p.Pro335Thr (c.1003C>A) in the general population?

CHST7 p.Pro335Thr (c.1003C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CHST7 p.Pro335Thr (c.1003C>A)?

AlphaMissense predicts likely benign (score 0.0989) — an in-silico prediction, not a clinical call.

CHST7 p.Pro335Thr

c.1003C>A · rs2519300640 · VCV3144757

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0989 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,147,880)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0989	likely benign
REVEL	0.218	benign-leaning
SaProt	LLR -6.97	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 3.6	GERP 1.3, phastCons 1
Regional constraint	o/e 0.73	unconstrained · MANE · 1,017 bp · p 1.6e-06 · regional, not allelic
Overall
CADD	12.16	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

No allele count reported in gnomAD v4.1 (AN 1,147,880). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHST7
Protein: p.Pro335Thr
Coding: c.1003C>A
MANE Select: NM_019886
dbSNP: rs2519300640
Type: single nucleotide variant
Location: chrX:46574934 (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-pro335thr (accessed [today's date]).

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