Is CCDC117 p.Glu40Asp (c.120G>C) pathogenic?

CCDC117 p.Glu40Asp (c.120G>C) is classified Likely benign in CCDC117 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-22). AlphaMissense: likely benign (0.0882); Absent from gnomAD v4.1.

How common is CCDC117 p.Glu40Asp (c.120G>C) in the general population?

CCDC117 p.Glu40Asp (c.120G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCDC117 p.Glu40Asp (c.120G>C)?

AlphaMissense predicts likely benign (score 0.0882) — an in-silico prediction, not a clinical call.

CCDC117 p.Glu40Asp

c.120G>C · rs2518208142 · VCV2487709

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0882 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0882	likely benign
REVEL	0.065	moderately benign-leaning
SaProt	LLR -6.88	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 1.3	GERP 0.77, phastCons 0.85
Regional constraint	o/e 1.10	unconstrained · MANE · 13 kb · p 0.062 · regional, not allelic
Overall
CADD	12.85	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: CCDC117
Protein: p.Glu40Asp
Coding: c.120G>C
MANE Select: NM_173510
dbSNP: rs2518208142
Type: single nucleotide variant
Location: chr22:28772969 (GRCh38)
Gene constraint: LOEUF 0.254 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 60.99
Residue 40: the 'disordered' region

Full CCDC117 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC117 p.Ala55Val Uncertain significance ★ ⚠ same type
CCDC117 p.Arg146Gln Uncertain significance ★ ⚠ same type
CCDC117 p.Arg203Cys Uncertain significance ★ ⚠ same type
CCDC117 p.Arg203His Uncertain significance ★ ⚠ same type
CCDC117 p.Arg44Trp Uncertain significance ★ ⚠ same type
CCDC117 p.Arg48His Uncertain significance ★ ⚠ same type
CCDC117 p.Arg62Cys Uncertain significance ★ ⚠ same type
CCDC117 p.Arg6Gly Uncertain significance ★ ⚠ same type

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/ccdc117-p-glu40asp (accessed [today's date]).

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