Is AURKC p.Ile79Val (c.235A>G) pathogenic?

AURKC p.Ile79Val (c.235A>G) is classified Benign in AURKC (ClinVar, Single submitter, 2 submitters; last evaluated 2017-04-28). AlphaMissense: likely benign (0.2049); Rare (popmax 0.651%, afr); Associated with spermatogenic failure 5.

What condition is associated with AURKC p.Ile79Val (c.235A>G)?

AURKC p.Ile79Val (c.235A>G) is associated with spermatogenic failure 5 (ClinVar).

How common is AURKC p.Ile79Val (c.235A>G) in the general population?

AURKC p.Ile79Val (c.235A>G) is rare (popmax 0.651%, afr) (gnomAD).

What do computational predictors say about AURKC p.Ile79Val (c.235A>G)?

AlphaMissense predicts likely benign (score 0.2049) — an in-silico prediction, not a clinical call.

AURKC p.Ile79Val

c.235A>G · rs61736320 · VCV893063

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2049 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.651%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

spermatogenic failure 5

Computational evidence

Protein change
AlphaMissense	0.2049	likely benign
REVEL	0.078	moderately benign-leaning
SaProt	LLR -7.61	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 0.24	GERP -0.48, phastCons 0.65
Regional constraint	o/e 0.87	unconstrained · MANE · 4,165 bp · p 0.0089 · regional, not allelic
Overall
CADD	16.88	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

Grpmax group 0.651% African / African-American · 488/75,012 alleles

Filtering AF 0.603% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.584%

Overall 0.0334% 539/1,614,124 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.651%	154
Remaining individualsnot grpmax-eligible	0.0528%	1,894
Admixed American	0.0217%	4,616
Middle Eastern	0.0165%	6,062
South Asian	0.0022%	45,538
European (non-Finnish)	0.000169%	590,009

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: AURKC
Protein: p.Ile79Val
Coding: c.235A>G
MANE Select: NM_001015878
dbSNP: rs61736320
Type: single nucleotide variant
Location: chr19:57232163 (GRCh38)
Gene constraint: LOEUF 0.806 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.25 · 3 PDB
Residue 79: the protein kinase domain; an α-helix

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

Disease context

spermatogenic failure 5 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Male infertility with teratozoospermia due to single gene mutation (Orphanet):

Onset: Adolescent, Adult

Similar variants

AURKC p.Tyr248Ter Pathogenic ★★ same condition
AURKC c.436-4A>G Uncertain significance ★★ same condition
AURKC p.Ile225= Uncertain significance ★★ same condition
AURKC p.Val254= Uncertain significance ★★ same condition
AURKC c.-128C>T Benign ★★ same condition
AURKC c.-145G>C Benign ★★ same condition
AURKC c.*38G>A Benign ★★ same condition
AURKC p.Leu132= Benign/Likely benign ★★ 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/aurkc-p-ile79val (accessed [today's date]).

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