Is TULP1 p.Gln485fs (c.1453_1460del) pathogenic?

TULP1 p.Gln485fs (c.14531460del) is classified Pathogenic/Likely pathogenic in TULP1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-05-15). Very rare (popmax 8.47e-05%, nfe); Associated with TULP1-related disorder.

What condition is associated with TULP1 p.Gln485fs (c.1453_1460del)?

TULP1 p.Gln485fs (c.1453_1460del) is associated with TULP1-related disorder (ClinVar).

How common is TULP1 p.Gln485fs (c.1453_1460del) in the general population?

TULP1 p.Gln485fs (c.1453_1460del) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

TULP1 p.Gln485fs

c.1453_1460del · rs1421431727 · VCV1950198

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

TULP1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon within the last 50 nt of the penultimate exon (14 of 15, 35 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -20	GERP -4.2

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,032 alleles

Overall 6.84e-05% 1/1,461,864 alleles · very rare

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: TULP1
Protein: p.Gln485fs
Coding: c.1453_1460del
MANE Select: NM_003322
dbSNP: rs1421431727
Type: Deletion
Location: chr6:35500016 (GRCh38)
Gene constraint: LOEUF 1.019 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.10 · 2 PDB

Full TULP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

TULP1-related disorder

Similar variants

TULP1 p.Arg419fs Pathogenic/Likely pathogenic ★★ same condition
TULP1 p.Leu504fs Pathogenic ★★ same condition
TULP1 p.Lys274fs Pathogenic/Likely pathogenic ★★ same condition
TULP1 p.Ile459fs Likely pathogenic ★ same condition
TULP1 p.Pro356fs Likely pathogenic ★ same condition
TULP1 p.Pro84fs Likely pathogenic ★ same condition
TULP1 p.Val412fs Likely pathogenic ★ same condition
TULP1 c.1112+1G>A Likely pathogenic ★★ 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/tulp1-p-gln485fs (accessed [today's date]).

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