Is TMPO p.Leu110= (c.330A>G) pathogenic?

TMPO p.Leu110= (c.330A>G) is classified Likely benign in TMPO (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-05-22). Ultra-rare (popmax 0.0658%, mid); Associated with Loeys-Dietz syndrome 2.

What condition is associated with TMPO p.Leu110= (c.330A>G)?

TMPO p.Leu110= (c.330A>G) is associated with Loeys-Dietz syndrome 2 (ClinVar).

How common is TMPO p.Leu110= (c.330A>G) in the general population?

TMPO p.Leu110= (c.330A>G) is ultra-rare (popmax 0.0658%, mid) (gnomAD).

TMPO p.Leu110=

Q: How is Familial thoracic aortic aneurysm and aortic dissection inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.330A>G · rs776054749 · VCV511301

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0658%, mid)

Conditions

Loeys-Dietz syndrome 2

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 0.003	GERP -4.3, phastCons 0.039
Overall
CADD	7.552	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0658% Middle Eastern · 4/6,080 alleles

Filtering AF 0.0224% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0135%

Overall 0.00136% 22/1,613,810 alleles · ultra-rare exomes 18/1,461,576 · genomes 4/152,234 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0658%	1,520
Admixed American	0.00833%	12,002
African / African-American	0.00667%	14,986
Remaining individualsnot grpmax-eligible	0.0032%	31,235
East Asian	0.00223%	44,814
European (non-Finnish)	0.000424%	235,977

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: TMPO
Protein: p.Leu110=
Coding: c.330A>G
MANE Select: NM_001032283
dbSNP: rs776054749
Type: single nucleotide variant
Location: chr12:98527936 (GRCh38)
Gene constraint: LOEUF 0.736 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 60.49 · 14 PDB
Residue 110: the lem domain; the 'disordered' region; the 'nucleoplasmic' region

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

Disease context

Loeys-Dietz syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Familial thoracic aortic aneurysm and aortic dissection (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood

Similar variants

TMPO p.Leu110Ile Uncertain significance ★ ⚠ same residue
TMPO c.565+1005A>G Uncertain significance ★★ ⚠ same condition
TMPO c.565+1009T>C Uncertain significance ★★ ⚠ same condition
TMPO c.565+1012A>C Uncertain significance ★★ ⚠ same condition
TMPO c.565+1017A>G Uncertain significance ★★ ⚠ same condition
TMPO c.565+1026A>G Uncertain significance ★★ ⚠ same condition
TMPO c.565+1029G>T Uncertain significance ★★ ⚠ same condition
TMPO c.565+1048G>C Uncertain significance ★★ ⚠ 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/tmpo-p-leu110 (accessed [today's date]).

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