Is STN1 p.Val22= (c.66G>A) pathogenic?

STN1 p.Val22= (c.66G>A) is classified Likely benign in STN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-17). Absent from gnomAD v4.1.

How common is STN1 p.Val22= (c.66G>A) in the general population?

STN1 p.Val22= (c.66G>A) is absent from gnomAD v4.1 (gnomAD).

STN1 p.Val22=

c.66G>A · rs2134380642 · VCV1635072

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 0.94	GERP -1.2, phastCons 1
Overall
CADD	11.61	PHRED · no single calibrated threshold — expert panels disagree

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: STN1
Protein: p.Val22=
Coding: c.66G>A
MANE Select: NM_024928
dbSNP: rs2134380642
Type: single nucleotide variant
Location: chr10:103917529 (GRCh38)
Gene constraint: LOEUF 0.975 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.67 · 8 PDB
Residue 22: an α-helix; the 'interaction with ctc1' region

Full STN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

STN1 p.Ala192Thr Uncertain significance ★★ ⚠ same type
STN1 p.Ala262Glu Uncertain significance ★★ ⚠ same type
STN1 p.Ala262Thr Uncertain significance ★★ ⚠ same type
STN1 p.Ala367Val Uncertain significance ★★ ⚠ same type
STN1 p.Arg133Gln Uncertain significance ★★ ⚠ same type
STN1 p.Arg295Gly Uncertain significance ★★ ⚠ same type
STN1 p.Arg306Trp Uncertain significance ★★ ⚠ same type
STN1 p.Arg332Cys 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/stn1-p-val22 (accessed [today's date]).

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