Is C2CD3 p.Ser787Phe (c.2360C>T) pathogenic?

C2CD3 p.Ser787Phe (c.2360C>T) is classified Uncertain significance in C2CD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-11-12). AlphaMissense: likely benign (0.1187); Ultra-rare (popmax 0.0257%, nfe); Associated with Inborn genetic diseases.

What condition is associated with C2CD3 p.Ser787Phe (c.2360C>T)?

C2CD3 p.Ser787Phe (c.2360C>T) is associated with Inborn genetic diseases (ClinVar).

How common is C2CD3 p.Ser787Phe (c.2360C>T) in the general population?

C2CD3 p.Ser787Phe (c.2360C>T) is ultra-rare (popmax 0.0257%, nfe) (gnomAD).

What do computational predictors say about C2CD3 p.Ser787Phe (c.2360C>T)?

AlphaMissense predicts likely benign (score 0.1187) — an in-silico prediction, not a clinical call.

C2CD3 p.Ser787Phe

c.2360C>T · rs145859522 · VCV2348119

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1187 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0257%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1187	likely benign
REVEL	0.094	moderately benign-leaning
SaProt	LLR -8.48	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 1.9, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 157 kb · p 9.8e-06 · regional, not allelic
Overall
CADD	22.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.0257% European (non-Finnish) · 303/1,180,054 alleles

Filtering AF 0.0232% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0223%

Overall 0.0195% 315/1,614,092 alleles · ultra-rare exomes 291/1,461,886 · genomes 24/152,206 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0257%	3,895
Remaining individualsnot grpmax-eligible	0.0112%	8,926
African / African-American	0.00667%	14,987

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: C2CD3
Protein: p.Ser787Phe
Coding: c.2360C>T
MANE Select: NM_001286577
dbSNP: rs145859522
Type: single nucleotide variant
Location: chr11:74103351 (GRCh38)
Gene constraint: LOEUF 0.637 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 55.65
Residue 787: the c2 2 domain

Full C2CD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

C2CD3 p.Ser787Cys Uncertain significance ★ ⚠ same residue
C2CD3 p.Ser787Ile Uncertain significance ★★ same residue
C2CD3 p.Ser787= Likely benign ★ same residue
C2CD3 c.2085+5G>A Uncertain significance ★★ same condition
C2CD3 c.4951+6C>T Uncertain significance ★★ same condition
C2CD3 p.Ala1382Pro Uncertain significance ★★ ⚠ same condition
C2CD3 p.Ala1777Thr Uncertain significance ★★ ⚠ same condition
C2CD3 p.Ala95Thr Uncertain significance ★★ ⚠ 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/c2cd3-p-ser787phe (accessed [today's date]).

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