Is AURKB p.Ser313= (c.939G>A) pathogenic?

AURKB p.Ser313= (c.939G>A) is classified Likely benign in AURKB (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-05-27). Very rare (popmax 0.00549%, sas); Associated with AURKB-related disorder.

What condition is associated with AURKB p.Ser313= (c.939G>A)?

AURKB p.Ser313= (c.939G>A) is associated with AURKB-related disorder (ClinVar).

How common is AURKB p.Ser313= (c.939G>A) in the general population?

AURKB p.Ser313= (c.939G>A) is very rare (popmax 0.00549%, sas) (gnomAD).

AURKB p.Ser313=

c.939G>A · rs754393355 · VCV3031939

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00549%, sas)

Conditions

AURKB-related disorder

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 -4.4	GERP -4.1
Overall
CADD	3.421	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00549% South Asian · 5/91,008 alleles

Filtering AF 0.00342% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0031%

Overall 0.0041% 66/1,610,034 alleles · very rare exomes 60/1,458,116 · genomes 6/151,918 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00549%	18,202
Admixed American	0.00517%	19,347
Remaining individualsnot grpmax-eligible	0.00482%	20,754
European (non-Finnish)	0.00441%	22,675
African / African-American	0.00403%	24,792

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: AURKB
Protein: p.Ser313=
Coding: c.939G>A
MANE Select: NM_004217
dbSNP: rs754393355
Type: single nucleotide variant
Location: chr17:8204967 (GRCh38)
Gene constraint: LOEUF 0.957 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.71 · 1 PDB
Residue 313: the protein kinase domain; an α-helix

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

Disease context

AURKB-related disorder

Similar variants

AURKB p.Gly212Arg Benign/Likely benign ★★ same type
AURKB p.Ala185Ser Uncertain significance ★ ⚠ same type
AURKB p.Arg159Cys Uncertain significance ★ ⚠ same type
AURKB p.Arg176Leu Uncertain significance ★ same type
AURKB p.Arg248Cys Uncertain significance ★ ⚠ same type
AURKB p.Arg309Ser Uncertain significance ★ ⚠ same type
AURKB p.Arg44Cys Uncertain significance ★ ⚠ same type
AURKB p.Arg95Gly 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/aurkb-p-ser313 (accessed [today's date]).

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