Is CEP57 p.Arg474= (c.1422G>A) pathogenic?

CEP57 p.Arg474= (c.1422G>A) is classified Likely benign in CEP57 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-03). Very rare (popmax 0.005%, amr); Associated with Inborn genetic diseases.

What condition is associated with CEP57 p.Arg474= (c.1422G>A)?

CEP57 p.Arg474= (c.1422G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CEP57 p.Arg474= (c.1422G>A) in the general population?

CEP57 p.Arg474= (c.1422G>A) is very rare (popmax 0.005%, amr) (gnomAD).

CEP57 p.Arg474=

c.1422G>A · VCV3832013

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP -0.23, phastCons 1
Overall
CADD	7.391	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/59,954 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.000274% 4/1,461,222 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.005%	19,985
European (non-Finnish)	8.48e-05%	1,179,636

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: CEP57
Protein: p.Arg474=
Coding: c.1422G>A
MANE Select: NM_014679
Type: single nucleotide variant
Location: chr11:95831175 (GRCh38)
Gene constraint: LOEUF 0.74 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.32 · 3 PDB
Residue 474: the 'mediates interaction with microtubules' region

Full CEP57 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

CEP57 p.Arg474Lys Uncertain significance ★ same residue
CEP57 p.Arg474Thr Uncertain significance ★ ⚠ same residue
CEP57 p.Ala19Gly Uncertain significance ★★ ⚠ same condition
CEP57 p.Ala278Thr Uncertain significance ★★ ⚠ same condition
CEP57 p.Ala412Thr Uncertain significance ★★ ⚠ same condition
CEP57 p.Ala4Gly Uncertain significance ★★ ⚠ same condition
CEP57 p.Ala4Val Uncertain significance ★★ ⚠ same condition
CEP57 p.Ala68Val 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/cep57-p-arg474 (accessed [today's date]).

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