Is CCDC115 p.Asp11Tyr (c.31G>T) pathogenic?

CCDC115 p.Asp11Tyr (c.31G>T) is classified Pathogenic in CCDC115 (ClinVar, No assertion criteria, 2 submitters; last evaluated 2019-06-21). AlphaMissense: likely pathogenic (0.7372); Absent from gnomAD v4.1; Associated with Congenital disorders of glycosylation type II.

What condition is associated with CCDC115 p.Asp11Tyr (c.31G>T)?

CCDC115 p.Asp11Tyr (c.31G>T) is associated with Congenital disorders of glycosylation type II, CCDC115-CDG (ClinVar).

How common is CCDC115 p.Asp11Tyr (c.31G>T) in the general population?

CCDC115 p.Asp11Tyr (c.31G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCDC115 p.Asp11Tyr (c.31G>T)?

AlphaMissense predicts likely pathogenic (score 0.7372) — an in-silico prediction, not a clinical call.

CCDC115 p.Asp11Tyr

c.31G>T · rs869025583 · VCV218963

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.7372 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Congenital disorders of glycosylation type II

Computational evidence

Protein change
AlphaMissense	0.7372	likely pathogenic ✓ concordant with ClinVar
REVEL	0.691	pathogenic-leaning
SaProt	LLR -14.65	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.7	phastCons 1
Regional constraint	o/e 1.07	unconstrained · MANE · 3,002 bp · p 0.28 · regional, not allelic
Overall
CADD	24.3	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CCDC115
Protein: p.Asp11Tyr
Coding: c.31G>T
MANE Select: NM_032357
dbSNP: rs869025583
Type: single nucleotide variant
Location: chr2:130342095 (GRCh38)
Gene constraint: LOEUF 1.198 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.32
Residue 11: a UniProt-annotated variant site (in cdg2o)

Full CCDC115 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Congenital disorders of glycosylation type II — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: CCDC115-CDG

Similar variants

VMA22 p.Leu31Ser Pathogenic ★★ same condition
VMA22 p.Arg102Gln Uncertain significance ★★ ⚠ same condition
CCDC115 p.Arg142Gln Uncertain significance ★ ⚠ same condition
CCDC115 p.Arg157His Uncertain significance ★ ⚠ same condition
VMA22 p.Arg157Cys Uncertain significance ★ ⚠ same condition
VMA22 p.Glu36Asp Uncertain significance ★ ⚠ same condition
VMA22 p.Ile151Leu Uncertain significance ★ ⚠ same condition
VMA22 p.Glu76fs 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/ccdc115-p-asp11tyr (accessed [today's date]).

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