Is CC2D2A p.Asp262= (c.786C>T) pathogenic?

CC2D2A p.Asp262= (c.786C>T) is classified Likely benign in CC2D2A (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-19). Rare (popmax 0.236%, eas); Associated with retinitis pigmentosa 93.

What condition is associated with CC2D2A p.Asp262= (c.786C>T)?

CC2D2A p.Asp262= (c.786C>T) is associated with retinitis pigmentosa 93, Meckel syndrome, type 6, Joubert syndrome 9 (ClinVar).

How common is CC2D2A p.Asp262= (c.786C>T) in the general population?

CC2D2A p.Asp262= (c.786C>T) is rare (popmax 0.236%, eas) (gnomAD).

How is Retinitis pigmentosa inherited?

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

CC2D2A p.Asp262=

c.786C>T · rs200434902 · VCV1109803

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.236%, eas)

Conditions

retinitis pigmentosa 93

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 -5.3
Overall
CADD	0.689	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.236% East Asian · 106/44,856 alleles

Filtering AF 0.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.186%

Overall 0.01% 162/1,612,980 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.236%	423
Middle Eastern	0.0165%	6,054
Remaining individualsnot grpmax-eligible	0.0144%	6,937
South Asian	0.00769%	12,997
Ashkenazi Jewishnot grpmax-eligible	0.00676%	14,787
European (non-Finnish)	0.00305%	32,755
Admixed American	0.00167%	59,994

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.Asp262=
Coding: c.786C>T
MANE Select: NM_001378615
dbSNP: rs200434902
Type: single nucleotide variant
Location: chr4:15514775 (GRCh38)
Gene constraint: LOEUF 0.854 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 69.46

Full CC2D2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

retinitis pigmentosa 93 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Meckel syndrome, type 6 Joubert syndrome 9 Joubert syndrome Meckel syndrome COACH syndrome 2

For Retinitis pigmentosa (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

CC2D2A p.Asp262Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
CC2D2A p.Asp262Glu Uncertain significance ★ ⚠ same residue
CC2D2A c.1017+1G>A Pathogenic/Likely pathogenic ★★ same condition
CC2D2A c.1149+1G>A Pathogenic/Likely pathogenic ★★ same condition
CC2D2A c.123+2T>G Likely pathogenic ★★ same condition
CC2D2A c.1359+1G>A Pathogenic/Likely pathogenic ★★ same condition
CC2D2A c.1359+1G>C Likely pathogenic ★★ same condition
CC2D2A c.1466+1G>A 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-asp262 (accessed [today's date]).

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