Is CC2D2A p.Pro619Ser (c.1855C>T) pathogenic?

CC2D2A p.Pro619Ser (c.1855C>T) is classified Uncertain significance in CC2D2A (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-05). AlphaMissense: likely pathogenic (0.7333); Very rare (popmax 0.00445%, sas); Associated with Joubert syndrome.

What condition is associated with CC2D2A p.Pro619Ser (c.1855C>T)?

CC2D2A p.Pro619Ser (c.1855C>T) is associated with Joubert syndrome, Meckel syndrome (ClinVar).

How common is CC2D2A p.Pro619Ser (c.1855C>T) in the general population?

CC2D2A p.Pro619Ser (c.1855C>T) is very rare (popmax 0.00445%, sas) (gnomAD).

What do computational predictors say about CC2D2A p.Pro619Ser (c.1855C>T)?

AlphaMissense predicts likely pathogenic (score 0.7333) — an in-silico prediction, not a clinical call.

CC2D2A p.Pro619Ser

c.1855C>T · rs1427654469 · VCV1035902

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7333 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00445%, sas)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Joubert syndrome

Computational evidence

Protein change
AlphaMissense	0.7333	likely pathogenic
REVEL	0.454	indeterminate
SaProt	LLR -12.35	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.5	GERP 2.4, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 104 kb · p 0.09 · regional, not allelic
Overall
CADD	23.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00445% South Asian · 4/89,886 alleles

Filtering AF 0.00144% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0009%

Overall 0.000311% 5/1,610,100 alleles · very rare exomes 5/1,457,834 · genomes 0/152,266 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00445%	22,472
European (non-Finnish)	8.49e-05%	1,178,307

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.Pro619Ser
Coding: c.1855C>T
MANE Select: NM_001378615
dbSNP: rs1427654469
Type: single nucleotide variant
Location: chr4:15537989 (GRCh38)
Gene constraint: LOEUF 0.854 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 69.46
Residue 619: the 'disordered' region

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

Disease context

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

Also linked: Meckel syndrome

Similar variants

CC2D2A p.Pro619Leu 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-pro619ser (accessed [today's date]).

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