Is CDC123 p.Asn271= (c.813C>T) pathogenic?

CDC123 p.Asn271= (c.813C>T) is classified Likely benign in CDC123 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-22). Ultra-rare (popmax 0.0445%, eas).

How common is CDC123 p.Asn271= (c.813C>T) in the general population?

CDC123 p.Asn271= (c.813C>T) is ultra-rare (popmax 0.0445%, eas) (gnomAD).

CDC123 p.Asn271=

c.813C>T · VCV4223143

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0445%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.01	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.33	GERP -4.1, phastCons 0.001
Overall
CADD	1.223	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0445% East Asian · 20/44,896 alleles

Filtering AF 0.0295% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0246%

Overall 0.00304% 49/1,613,984 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0445%	2,245
African / African-American	0.00668%	14,980
South Asian	0.00439%	22,771
European (non-Finnish)	0.00169%	59,001

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: CDC123
Protein: p.Asn271=
Coding: c.813C>T
MANE Select: NM_006023
Type: single nucleotide variant
Location: chr10:12246244 (GRCh38)
Gene constraint: LOEUF 1.013 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.82 · 2 PDB

Full CDC123 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDC123 c.489+3A>C Benign ★★ same type
CDC123 c.847-4A>G Benign ★★ same type
CDC123 p.Ala113Val Uncertain significance ★ ⚠ same type
CDC123 p.Ala279Thr Uncertain significance ★ ⚠ same type
CDC123 p.Ala319Thr Uncertain significance ★ ⚠ same type
CDC123 p.Arg142Gly Uncertain significance ★ ⚠ same type
CDC123 p.Arg142His Uncertain significance ★ ⚠ same type
CDC123 p.Arg167Gln 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/cdc123-p-asn271 (accessed [today's date]).

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