Is CHST9 p.Val7Phe (c.19G>T) pathogenic?

CHST9 p.Val7Phe (c.19G>T) is classified Uncertain significance in CHST9 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-20). AlphaMissense: likely benign (0.1083); Absent from gnomAD v4.1.

How common is CHST9 p.Val7Phe (c.19G>T) in the general population?

CHST9 p.Val7Phe (c.19G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CHST9 p.Val7Phe (c.19G>T)?

AlphaMissense predicts likely benign (score 0.1083) — an in-silico prediction, not a clinical call.

CHST9 p.Val7Phe

c.19G>T · rs2058578953 · VCV3144779

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1083 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1083	likely benign
REVEL	0.185	benign-leaning
SaProt	LLR -6.81	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 7.6	GERP 2.7, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 227 kb · p 0.58 · regional, not allelic
Overall
CADD	25.2	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CHST9
Protein: p.Val7Phe
Coding: c.19G>T
MANE Select: NM_031422
dbSNP: rs2058578953
Type: single nucleotide variant
Location: chr18:27142791 (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.Pro393= Benign ★★ same type
CHST9 p.Arg62Trp Uncertain significance ★ ⚠ 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-val7phe (accessed [today's date]).

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