Is STK10 p.Phe3Ser (c.8T>C) pathogenic?

STK10 p.Phe3Ser (c.8T>C) is classified Uncertain significance in STK10 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-22). AlphaMissense: likely pathogenic (0.9851); Absent from gnomAD v4.1.

How common is STK10 p.Phe3Ser (c.8T>C) in the general population?

STK10 p.Phe3Ser (c.8T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about STK10 p.Phe3Ser (c.8T>C)?

AlphaMissense predicts likely pathogenic (score 0.9851) — an in-silico prediction, not a clinical call.

STK10 p.Phe3Ser

c.8T>C · VCV4590600

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9851 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.9851	likely pathogenic · top 10% in STK10
REVEL	0.521	indeterminate
SaProt	LLR -9.02	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.6, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 113 bp · p 0.64 · regional, not allelic
Overall
CADD	29.4	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: STK10
Protein: p.Phe3Ser
Coding: c.8T>C
MANE Select: NM_005990
Type: single nucleotide variant
Location: chr5:172188035 (GRCh38)
Gene constraint: LOEUF 0.85 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.82 · 14 PDB

Full STK10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

STK10 p.Ala286Val Uncertain significance ★ ⚠ same type
STK10 p.Ala420Gly Uncertain significance ★ ⚠ same type
STK10 p.Ala456Thr Uncertain significance ★ ⚠ same type
STK10 p.Ala632Val Uncertain significance ★ ⚠ same type
STK10 p.Ala833Thr Uncertain significance ★ ⚠ same type
STK10 p.Arg11His Uncertain significance ★ ⚠ same type
STK10 p.Arg11Leu Uncertain significance ★ ⚠ same type
STK10 p.Arg139Cys 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/stk10-p-phe3ser (accessed [today's date]).

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