Is CCDC18 p.Asn314= (c.942C>T) pathogenic?

CCDC18 p.Asn314= (c.942C>T) is classified Benign in CCDC18 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-21). Common (popmax 32%, amr) — too common for a highly-penetrant pathogenic allele; Associated with CCDC18-related disorder.

What condition is associated with CCDC18 p.Asn314= (c.942C>T)?

CCDC18 p.Asn314= (c.942C>T) is associated with CCDC18-related disorder (ClinVar).

CCDC18 p.Asn314=

Q: How common is CCDC18 p.Asn314= (c.942C>T) in the general population?

CCDC18 p.Asn314= (c.942C>T) is common (popmax 32%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.942C>T · rs2783499 · VCV3060341

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 32%, amr) — too common for a highly-penetrant pathogenic allele

Conditions

CCDC18-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.043	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.9	GERP -2.3, phastCons 0.76
Overall
CADD	9.315	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 32% Admixed American · 15,682/48,986 alleles

Filtering AF 31.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 31.4%

Overall 17.3% 259,764/1,502,798 alleles · common

Ancestry group	Frequency	1 in
Admixed Americangrpmax	32%	3
East Asian	31.6%	3
South Asian	27.7%	4
African / African-American	18%	6
Middle Eastern	17.6%	6
Remaining individualsnot grpmax-eligible	17.6%	6
Finnishnot grpmax-eligible	16.9%	6
European (non-Finnish)	15.5%	6
Amishnot grpmax-eligible	13.5%	7
Ashkenazi Jewishnot grpmax-eligible	10.8%	9

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: CCDC18
Protein: p.Asn314=
Coding: c.942C>T
MANE Select: NM_001378204
dbSNP: rs2783499
Type: single nucleotide variant
Location: chr1:93207131 (GRCh38)
Gene constraint: LOEUF 0.901 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.83

Full CCDC18 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CCDC18-related disorder

Similar variants

CCDC18 c.2982-6T>C Likely benign same condition
CCDC18 c.569+9A>G Benign same condition
CCDC18 p.Ala153= Likely benign same condition
CCDC18 p.Arg1108= Benign same condition
CCDC18 p.Arg1108Ser Benign same condition
CCDC18 p.Arg1281= Benign same condition
CCDC18 p.Arg429Cys Benign same condition
CCDC18 p.Asn326Thr Benign ⚠ 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/ccdc18-p-asn314 (accessed [today's date]).

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