CC2D2A p.Asp1038=
c.3114T>C · rs781371086 · VCV702914
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00335%, amr)
Conditions
2
Joubert syndrome
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 -3.7 | GERP -5.5 |
| Overall | ||
| CADD | 2.956 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00335%
Admixed American · 2/59,746 alleles
Filtering AF
0.000555%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000429%
Overall
0.00118%
19/1,612,018 alleles · very rare
exomes 16/1,459,822 · genomes 3/152,196 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00335% | 29,873 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,203 |
| African / African-American | 0.00267% | 37,454 |
| South Asian | 0.0011% | 90,518 |
| European (non-Finnish) | 0.00102% | 98,266 |
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
- CC2D2A
- Protein
- p.Asp1038=
- Coding
- c.3114T>C
- MANE Select
- NM_001378615
- dbSNP
- rs781371086
- Type
- single nucleotide variant
- Location
- chr4:15563454 (GRCh38)
- Gene constraint
- LOEUF 0.854 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 69.46
- Residue 1038
- the c2 domain
Similar variants
- CC2D2A p.Asp1038Val Uncertain significance ★★ same residue
- CC2D2A c.1017+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CC2D2A c.123+2T>G Likely pathogenic ★★ same condition
- CC2D2A c.1359+1G>C Likely pathogenic ★★ same condition
- CC2D2A c.1466+1G>A Likely pathogenic ★★ same condition
- CC2D2A c.1466+2T>C Likely pathogenic ★★ same condition
- CC2D2A c.1608-2A>G Likely pathogenic ★★ same condition
- CC2D2A c.2004-17A>G 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/cc2d2a-p-asp1038 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown