Is CSPP1 p.Asp1086= (c.3258C>T) pathogenic?

CSPP1 p.Asp1086= (c.3258C>T) is classified Likely benign in CSPP1 (ClinVar, Single submitter, 2 submitters; last evaluated 2024-02-23). Very rare (popmax 0.0022%, sas); Associated with Joubert syndrome 21.

What condition is associated with CSPP1 p.Asp1086= (c.3258C>T)?

CSPP1 p.Asp1086= (c.3258C>T) is associated with Joubert syndrome 21 (ClinVar).

How common is CSPP1 p.Asp1086= (c.3258C>T) in the general population?

CSPP1 p.Asp1086= (c.3258C>T) is very rare (popmax 0.0022%, sas) (gnomAD).

CSPP1 p.Asp1086=

c.3258C>T · rs769247285 · VCV1109201

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Conditions

Joubert syndrome 21

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -4	GERP -3.8
Overall
CADD	0.909	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/91,084 alleles

Filtering AF 0.000953% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000787%

Overall 0.00124% 20/1,613,976 alleles · very rare exomes 19/1,461,826 · genomes 1/152,150 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0022%	45,542
European (non-Finnish)	0.00153%	65,554

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: CSPP1
Protein: p.Asp1086=
Coding: c.3258C>T
MANE Select: NM_001382391
dbSNP: rs769247285
Type: single nucleotide variant
Location: chr8:67190687 (GRCh38)

Full CSPP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Joubert syndrome 21 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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/cspp1-p-asp1086 (accessed [today's date]).

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