Is CSPP1 p.Lys35Arg (c.104A>G) pathogenic?

CSPP1 p.Lys35Arg (c.104A>G) is classified Conflicting classifications of pathogenicity in CSPP1 (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-01-12). Rare (popmax 0.37%, sas); Associated with Joubert syndrome 21.

What condition is associated with CSPP1 p.Lys35Arg (c.104A>G)?

CSPP1 p.Lys35Arg (c.104A>G) is associated with Joubert syndrome 21 (ClinVar).

How common is CSPP1 p.Lys35Arg (c.104A>G) in the general population?

CSPP1 p.Lys35Arg (c.104A>G) is rare (popmax 0.37%, sas) (gnomAD).

CSPP1 p.Lys35Arg

c.104A>G · rs200158932 · VCV446051

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.37%, sas)

Conditions

Joubert syndrome 21

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
REVEL	0.081	moderately benign-leaning
Splicing
SpliceAI	Δ0.32	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 4.5	GERP 0.54, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 121 kb · p 0.15 · regional, not allelic
Overall
CADD	24.0	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.37% South Asian · 313/84,702 alleles

Filtering AF 0.336% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.323%

Overall 0.0751% 1,180/1,571,978 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.515%	194
South Asiangrpmax	0.37%	271
Middle Eastern	0.187%	534
Admixed American	0.127%	790
Remaining individualsnot grpmax-eligible	0.125%	799
European (non-Finnish)	0.0486%	2,058
African / African-American	0.00689%	14,509
Finnishnot grpmax-eligible	0.00158%	63,182

Ashkenazi Jewish 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: CSPP1
Protein: p.Lys35Arg
Coding: c.104A>G
MANE Select: NM_001382391
dbSNP: rs200158932
Type: single nucleotide variant
Location: chr8:67076486 (GRCh38)
Gene constraint: LOEUF 0.876 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 57.34

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

Similar variants

CSPP1 c.1022+1G>T Likely pathogenic ★★ same condition
CSPP1 c.1187+1G>A Pathogenic/Likely pathogenic ★★ same condition
CSPP1 c.1497-2A>C Likely pathogenic ★★ same condition
CSPP1 c.1697+1G>T Pathogenic/Likely pathogenic ★★ same condition
CSPP1 c.2968+1G>A Pathogenic ★★ same condition
CSPP1 c.2968+1G>T Pathogenic ★★ same condition
CSPP1 c.923+1G>C Pathogenic ★★ same condition
CSPP1 c.-69C>T Pathogenic/Likely pathogenic ★★ 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/cspp1-p-lys35arg (accessed [today's date]).

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