Is CCDC124 p.Glu118Lys (c.352G>A) pathogenic?

CCDC124 p.Glu118Lys (c.352G>A) is classified Uncertain significance in CCDC124 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-28). AlphaMissense: likely benign (0.0877); Absent from gnomAD v4.1.

How common is CCDC124 p.Glu118Lys (c.352G>A) in the general population?

CCDC124 p.Glu118Lys (c.352G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCDC124 p.Glu118Lys (c.352G>A)?

AlphaMissense predicts likely benign (score 0.0877) — an in-silico prediction, not a clinical call.

CCDC124 p.Glu118Lys

c.352G>A · rs1384214143 · VCV2490185

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0877 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 166,464)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0877	likely benign
REVEL	0.041	moderately benign-leaning
SaProt	LLR -5.65	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.70 · evaluated, not missing
Constraint at this position
Conservation	phyloP 9.6	phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 7,291 bp · p 0.057 · regional, not allelic
Overall
CADD	22.2	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

No allele count reported in gnomAD v4.1 (AN 166,464). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CCDC124
Protein: p.Glu118Lys
Coding: c.352G>A
MANE Select: NM_001136203
dbSNP: rs1384214143
Type: single nucleotide variant
Location: chr19:17943263 (GRCh38)
Gene constraint: LOEUF 0.991 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 80.59 · 6 PDB
Residue 118: the 'disordered' region

Full CCDC124 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC124 p.Ala160Val Uncertain significance ★ ⚠ same type
CCDC124 p.Ala161Val Uncertain significance ★ ⚠ same type
CCDC124 p.Ala26Pro Uncertain significance ★ ⚠ same type
CCDC124 p.Ala26Thr Uncertain significance ★ ⚠ same type
CCDC124 p.Ala86Thr Uncertain significance ★ ⚠ same type
CCDC124 p.Ala98Val Uncertain significance ★ ⚠ same type
CCDC124 p.Arg106Gln Uncertain significance ★ ⚠ same type
CCDC124 p.Arg145His 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/ccdc124-p-glu118lys (accessed [today's date]).

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