Is CHST7 p.Leu331= (c.993G>T) pathogenic?

CHST7 p.Leu331= (c.993G>T) is classified Likely benign in CHST7 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-01). Absent from gnomAD v4.1.

How common is CHST7 p.Leu331= (c.993G>T) in the general population?

CHST7 p.Leu331= (c.993G>T) is absent from gnomAD v4.1 (gnomAD).

CHST7 p.Leu331=

c.993G>T · rs1942489234 · VCV2660383

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,142,378)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.73	GERP -1.4, phastCons 1
Overall
CADD	6.187	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,142,378). 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.Leu331=
Coding: c.993G>T
MANE Select: NM_019886
dbSNP: rs1942489234
Type: single nucleotide variant
Location: chrX:46574924 (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-leu331 (accessed [today's date]).

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