Is LATS2 p.Pro307Ser (c.919C>T) pathogenic?

LATS2 p.Pro307Ser (c.919C>T) is classified Uncertain significance in LATS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-03). AlphaMissense: likely benign (0.0635); Absent from gnomAD v4.1.

How common is LATS2 p.Pro307Ser (c.919C>T) in the general population?

LATS2 p.Pro307Ser (c.919C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about LATS2 p.Pro307Ser (c.919C>T)?

AlphaMissense predicts likely benign (score 0.0635) — an in-silico prediction, not a clinical call.

LATS2 p.Pro307Ser

c.919C>T · rs779525816 · VCV3117967

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0635 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0635	likely benign
REVEL	0.023	moderately benign-leaning
SaProt	LLR -7.29	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 0.037	GERP -2.9
Regional constraint	o/e 1.07	unconstrained · MANE · 1,339 bp · p 0.056 · regional, not allelic
Overall
CADD	0.535	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

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: LATS2
Protein: p.Pro307Ser
Coding: c.919C>T
MANE Select: NM_014572
dbSNP: rs779525816
Type: single nucleotide variant
Location: chr13:20988861 (GRCh38)
Gene constraint: LOEUF 0.493 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 56.73 · 1 PDB
Residue 307: the 'disordered' region

Full LATS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

LATS2 c.2665+5A>G Benign ★★ same type
LATS2 p.Arg378= Benign/Likely benign ★★ same type
LATS2 p.Asp1013Asn Benign ★★ same type
LATS2 p.Asp534= Benign ★★ same type
LATS2 p.Asp852Glu Benign ★★ same type
LATS2 p.Gly563Arg Benign ★★ same type
LATS2 p.Leu386= Benign ★★ same type
LATS2 p.Pro280= Benign ★★ 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/lats2-p-pro307ser (accessed [today's date]).

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