Is CDCA5 p.Ser8Tyr (c.23C>A) pathogenic?

CDCA5 p.Ser8Tyr (c.23C>A) is classified Uncertain significance in CDCA5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-04). AlphaMissense: ambiguous (0.3614); Absent from gnomAD v4.1.

How common is CDCA5 p.Ser8Tyr (c.23C>A) in the general population?

CDCA5 p.Ser8Tyr (c.23C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDCA5 p.Ser8Tyr (c.23C>A)?

AlphaMissense predicts ambiguous (score 0.3614) — an in-silico prediction, not a clinical call.

CDCA5 p.Ser8Tyr

c.23C>A · VCV3829931

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3614 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,594,450)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.3614	ambiguous
REVEL	0.094	moderately benign-leaning
SaProt	LLR -11.53	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call.
Splicing
SpliceAI	Δ0.28	donor gain · deltas
Pangolin	Δ0.21	gain · loss 0.02 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 8.1	GERP 1, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 4,868 bp · p 0.33 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

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 1,594,450). 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: CDCA5
Protein: p.Ser8Tyr
Coding: c.23C>A
MANE Select: NM_080668
Type: single nucleotide variant
Location: chr11:65083956 (GRCh38)
Gene constraint: LOEUF 0.88 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.04
Residue 8: the 'disordered' region

Full CDCA5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDCA5 p.Glu123Lys Benign ★★ same type
CDCA5 p.Gly173= Benign ★★ same type
CDCA5 p.Gly179Arg Benign ★★ same type
CDCA5 p.Pro120= Benign ★★ same type
CDCA5 p.Thr105= Benign ★★ same type
CDCA5 p.Ala51Thr Uncertain significance ★ ⚠ same type
CDCA5 p.Arg148Trp Uncertain significance ★ ⚠ same type
CDCA5 p.Arg4Gly 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/cdca5-p-ser8tyr (accessed [today's date]).

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