Is C2CD3 p.Gly1337Arg (c.4009G>A) pathogenic?

C2CD3 p.Gly1337Arg (c.4009G>A) is classified Uncertain significance in C2CD3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-13). AlphaMissense: likely pathogenic (0.912); Very rare (popmax 0.00363%, amr); Associated with Inborn genetic diseases.

What condition is associated with C2CD3 p.Gly1337Arg (c.4009G>A)?

C2CD3 p.Gly1337Arg (c.4009G>A) is associated with Inborn genetic diseases (ClinVar).

How common is C2CD3 p.Gly1337Arg (c.4009G>A) in the general population?

C2CD3 p.Gly1337Arg (c.4009G>A) is very rare (popmax 0.00363%, amr) (gnomAD).

What do computational predictors say about C2CD3 p.Gly1337Arg (c.4009G>A)?

AlphaMissense predicts likely pathogenic (score 0.912) — an in-silico prediction, not a clinical call.

C2CD3 p.Gly1337Arg

c.4009G>A · rs767852213 · VCV2077499

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.912 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00363%, amr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.912	likely pathogenic · top 6% in C2CD3
REVEL	0.554	indeterminate
SaProt	LLR -8.59	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.27 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.7	GERP 1.6, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 157 kb · p 9.8e-06 · regional, not allelic
Overall
CADD	25.8	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00363% Admixed American · 2/55,072 alleles

Filtering AF 0.00104% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000835%

Overall 0.00151% 24/1,594,308 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00363%	27,536
Remaining individualsnot grpmax-eligible	0.00162%	61,556
European (non-Finnish)	0.00162%	61,707
Finnishnot grpmax-eligible	0.00158%	63,364
African / African-American	0.00136%	73,770

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.Gly1337Arg
Coding: c.4009G>A
MANE Select: NM_001286577
dbSNP: rs767852213
Type: single nucleotide variant
Location: chr11:74078709 (GRCh38)
Gene constraint: LOEUF 0.637 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 55.65
Residue 1337: the c2 4 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 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
C2CD3 p.Arg1122Ile Uncertain significance ★★ ⚠ same condition
C2CD3 p.Arg1145His Uncertain significance ★★ ⚠ same condition
C2CD3 p.Arg1183His 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-gly1337arg (accessed [today's date]).

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