Is STN1 p.Val232= (c.696G>C) pathogenic?

STN1 p.Val232= (c.696G>C) is classified Benign in STN1 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-04). Common (popmax 23%, nfe) — too common for a highly-penetrant pathogenic allele; Associated with cerebroretinal microangiopathy with calcifications and cysts 2.

What condition is associated with STN1 p.Val232= (c.696G>C)?

STN1 p.Val232= (c.696G>C) is associated with cerebroretinal microangiopathy with calcifications and cysts 2 (ClinVar).

How is Coats plus syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

STN1 p.Val232=

Q: How common is STN1 p.Val232= (c.696G>C) in the general population?

STN1 p.Val232= (c.696G>C) is common (popmax 23%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.696G>C · rs11191853 · VCV1169156

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 23%, nfe) — too common for a highly-penetrant pathogenic allele

Conditions

cerebroretinal microangiopathy with calcifications and cysts 2

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 3.3	GERP 0.84, phastCons 1
Overall
CADD	9.442	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 23% European (non-Finnish) · 271,909/1,179,712 alleles

Filtering AF 23% ClinGen BA1/BS1 input FAF95, joint · FAF99 22.9%

Overall 22% 355,030/1,613,694 alleles · common

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	38.3%	3
European (non-Finnish)grpmax	23%	4
Ashkenazi Jewishnot grpmax-eligible	22.8%	4
Remaining individualsnot grpmax-eligible	22.2%	5
Finnishnot grpmax-eligible	22.1%	5
African / African-American	21.1%	5
Admixed American	21.1%	5
Middle Eastern	20.5%	5
East Asian	15.8%	6
South Asian	12.3%	8

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: STN1
Protein: p.Val232=
Coding: c.696G>C
MANE Select: NM_024928
dbSNP: rs11191853
Type: single nucleotide variant
Location: chr10:103897605 (GRCh38)
Gene constraint: LOEUF 0.975 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.67 · 8 PDB
Residue 232: the 'winged helix-turn-helix (whth) 1' region

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

Disease context

cerebroretinal microangiopathy with calcifications and cysts 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Coats plus syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood
Prevalence: <1 / 1 000 000 (Europe)

Similar variants

STN1 p.Ala367Val Uncertain significance ★★ ⚠ same condition
STN1 p.Arg133Gln Uncertain significance ★★ ⚠ same condition
STN1 p.Arg7Trp Uncertain significance ★★ ⚠ same condition
STN1 p.Asp70Glu Uncertain significance ★★ ⚠ same condition
STN1 c.582-4G>A Benign/Likely benign ★★ same condition
STN1 p.Ser248Cys Benign ★★ same condition
STN1 p.Thr151Ala Benign ★★ same condition
STN1 p.Asp157Tyr Uncertain significance ★ ⚠ same condition

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-val232 (accessed [today's date]).

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