Is CDK10 p.Ser355Arg (c.1065C>A) pathogenic?

CDK10 p.Ser355Arg (c.1065C>A) is classified Uncertain significance in CDK10 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-02). AlphaMissense: likely benign (0.1938); Absent from gnomAD v4.1; Associated with Al Kaissi syndrome.

What condition is associated with CDK10 p.Ser355Arg (c.1065C>A)?

CDK10 p.Ser355Arg (c.1065C>A) is associated with Al Kaissi syndrome (ClinVar).

How common is CDK10 p.Ser355Arg (c.1065C>A) in the general population?

CDK10 p.Ser355Arg (c.1065C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDK10 p.Ser355Arg (c.1065C>A)?

AlphaMissense predicts likely benign (score 0.1938) — an in-silico prediction, not a clinical call.

CDK10 p.Ser355Arg

c.1065C>A · rs2060691897 · VCV1027758

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1938 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,600,344)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Al Kaissi syndrome

Computational evidence

Protein change
AlphaMissense	0.1938	likely benign
REVEL	0.046	moderately benign-leaning
SaProt	LLR -7.42	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.9	GERP 0.016, phastCons 1
Regional constraint	o/e 1.21	unconstrained · MANE · 8,978 bp · p 2.4e-06 · regional, not allelic
Overall
CADD	20.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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 1,600,344). 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: CDK10
Protein: p.Ser355Arg
Coding: c.1065C>A
MANE Select: NM_052988
dbSNP: rs2060691897
Type: single nucleotide variant
Location: chr16:89695674 (GRCh38)
Gene constraint: LOEUF 1.344 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.27
Residue 355: the 'disordered' region

Full CDK10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Al Kaissi syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDK10 c.608+1G>A Pathogenic ★★ same condition
CDK10 c.609-1G>A Pathogenic/Likely pathogenic ★★ same condition
CDK10 c.87+5G>A Pathogenic/Likely pathogenic ★★ same condition
CDK10 p.Cys8Ter Pathogenic/Likely pathogenic ★★ same condition
CDK10 p.Arg57Trp Uncertain significance ★★ same condition
CDK10 p.Asp221Asn Uncertain significance ★★ ⚠ same condition
CDK10 p.Cys176Ser Uncertain significance ★★ ⚠ same condition
CDK10 p.Glu9Gln 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/cdk10-p-ser355arg (accessed [today's date]).

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