Is THOC2 p.Phe45Ile (c.133T>A) pathogenic?

THOC2 p.Phe45Ile (c.133T>A) is classified Uncertain significance in THOC2 (ClinVar, Single submitter, 2 submitters). AlphaMissense: likely benign (0.09); Absent from gnomAD v4.1; Associated with X-linked intellectual disability-short stature-overweight syndrome.

What condition is associated with THOC2 p.Phe45Ile (c.133T>A)?

THOC2 p.Phe45Ile (c.133T>A) is associated with X-linked intellectual disability-short stature-overweight syndrome (ClinVar).

How common is THOC2 p.Phe45Ile (c.133T>A) in the general population?

THOC2 p.Phe45Ile (c.133T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about THOC2 p.Phe45Ile (c.133T>A)?

AlphaMissense predicts likely benign (score 0.09) — an in-silico prediction, not a clinical call.

THOC2 p.Phe45Ile

c.133T>A · rs1569441509 · VCV592093

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.09 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

X-linked intellectual disability-short stature-overweight syndrome

Computational evidence

Protein change
AlphaMissense	0.09	likely benign
REVEL	0.144	moderately benign-leaning
SaProt	LLR -5.48	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 6	GERP 0.88, phastCons 1
Regional constraint	o/e 0.72	unconstrained · MANE · 35 kb · p 0.011 · regional, not allelic
Overall
CADD	17.72	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: THOC2
Protein: p.Phe45Ile
Coding: c.133T>A
MANE Select: NM_001081550
dbSNP: rs1569441509
Type: single nucleotide variant
Location: chrX:123706947 (GRCh38)
Structure: AlphaFold pLDDT 72.83 · 4 PDB
Residue 45: the 'anchor domain; interaction with thoc5 and thoc7' region; an α-helix

Full THOC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

X-linked intellectual disability-short stature-overweight syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

THOC2 p.Cys615Tyr Likely pathogenic ★★ same condition
THOC2 p.Thr696Ile Pathogenic/Likely pathogenic ★★ same condition
THOC2 p.Ala912Pro Uncertain significance ★★ ⚠ same condition
THOC2 p.Asn208Ser Uncertain significance ★★ ⚠ same condition
THOC2 p.Asp656Gly Uncertain significance ★★ ⚠ same condition
THOC2 p.Gly1205Arg Uncertain significance ★★ same condition
THOC2 p.Pro1416Ser Uncertain significance ★★ ⚠ same condition
THOC2 c.2317-47A>G 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/thoc2-p-phe45ile (accessed [today's date]).

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