Is CDK19 p.Arg501Gln (c.1502G>A) pathogenic?

CDK19 p.Arg501Gln (c.1502G>A) is classified Uncertain significance in CDK19 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-02). AlphaMissense: likely benign (0.1422); Very rare (popmax 0.00288%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CDK19 p.Arg501Gln (c.1502G>A)?

CDK19 p.Arg501Gln (c.1502G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CDK19 p.Arg501Gln (c.1502G>A) in the general population?

CDK19 p.Arg501Gln (c.1502G>A) is very rare (popmax 0.00288%, nfe) (gnomAD).

What do computational predictors say about CDK19 p.Arg501Gln (c.1502G>A)?

AlphaMissense predicts likely benign (score 0.1422) — an in-silico prediction, not a clinical call.

CDK19 p.Arg501Gln

c.1502G>A · rs776325246 · VCV3141534

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1422 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00288%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1422	likely benign
REVEL	0.287	benign-leaning
SaProt	LLR -8.74	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 7.7	GERP 2.7, phastCons 1
Regional constraint	o/e 0.70	unconstrained · MANE · 8,332 bp · p 5.7e-06 · regional, not allelic
Overall
CADD	25.5	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

Grpmax group 0.00288% European (non-Finnish) · 34/1,179,884 alleles

Filtering AF 0.00207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00183%

Overall 0.00217% 35/1,613,754 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00288%	34,702
Remaining individualsnot grpmax-eligible	0.0016%	62,468

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: CDK19
Protein: p.Arg501Gln
Coding: c.1502G>A
MANE Select: NM_015076
dbSNP: rs776325246
Type: single nucleotide variant
Location: chr6:110614542 (GRCh38)
Gene constraint: LOEUF 0.655 · pLI 0.49 (gnomAD)
Structure: AlphaFold pLDDT 77.97
Residue 501: the 'disordered' region

Full CDK19 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

CDK19 p.Thr196Ala Pathogenic/Likely pathogenic ★★ ⚠ same condition
CDK19 p.Lys47Asn Uncertain significance ★★ ⚠ same condition
CDK19 p.Pro495Thr Uncertain significance ★★ ⚠ same condition
CDK19 p.Arg112Cys Uncertain significance ★ ⚠ same condition
CDK19 p.Arg166Met Uncertain significance ★ ⚠ same condition
CDK19 p.Arg441Gln Uncertain significance ★ ⚠ same condition
CDK19 p.Arg464Cys Uncertain significance ★ ⚠ same condition
CDK19 p.Arg464His 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/cdk19-p-arg501gln (accessed [today's date]).

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