Is CEP63 p.Arg11Ter (c.31C>T) pathogenic?

CEP63 p.Arg11Ter (c.31C>T) is classified Conflicting classifications of pathogenicity in CEP63 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-10-18). Ultra-rare (popmax 0.0134%, afr); Associated with Inborn genetic diseases.

What condition is associated with CEP63 p.Arg11Ter (c.31C>T)?

CEP63 p.Arg11Ter (c.31C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CEP63 p.Arg11Ter (c.31C>T) in the general population?

CEP63 p.Arg11Ter (c.31C>T) is ultra-rare (popmax 0.0134%, afr) (gnomAD).

CEP63 p.Arg11Ter

c.31C>T · rs763001827 · VCV501990

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 15
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.1	GERP -0.14, phastCons 1
Overall
CADD	41.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% African / African-American · 10/74,812 alleles

Filtering AF 0.00724% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00551%

Overall 0.00186% 30/1,612,752 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0134%	7,481
Admixed American	0.005%	19,992
Remaining individualsnot grpmax-eligible	0.0016%	62,424
European (non-Finnish)	0.00127%	78,613
South Asian	0.0011%	90,952

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: CEP63
Protein: p.Arg11Ter
Coding: c.31C>T
MANE Select: NM_001353108
dbSNP: rs763001827
Type: single nucleotide variant
Location: chr3:134495351 (GRCh38)
Gene constraint: LOEUF 1.127 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.95 · 4 PDB

Full CEP63 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

CEP63 p.Arg11Gln Uncertain significance ★ ⚠ same residue
CEP63 p.Arg11= Likely benign ★ same residue
CEP63 p.Arg215Trp Uncertain significance ★★ ⚠ same condition
CEP63 p.Arg46His Uncertain significance ★★ ⚠ same condition
CEP63 p.Arg474His Uncertain significance ★★ ⚠ same condition
CEP63 p.Arg57His Uncertain significance ★★ ⚠ same condition
CEP63 p.Asn301Ile Uncertain significance ★★ ⚠ same condition
CEP63 p.Asn633Asp 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/cep63-p-arg11ter (accessed [today's date]).

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