Is TULP1 p.Thr55fs (c.162dup) pathogenic?

TULP1 p.Thr55fs (c.162dup) is classified Pathogenic/Likely pathogenic in TULP1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-08-09). Ultra-rare (gnomAD MAF 2.89e-06); Associated with retinitis pigmentosa 14.

What condition is associated with TULP1 p.Thr55fs (c.162dup)?

TULP1 p.Thr55fs (c.162dup) is associated with retinitis pigmentosa 14 (ClinVar).

How common is TULP1 p.Thr55fs (c.162dup) in the general population?

TULP1 p.Thr55fs (c.162dup) is ultra-rare (gnomAD MAF 2.89e-06) (gnomAD).

How is Retinitis pigmentosa inherited?

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

TULP1 p.Thr55fs

c.162dup · rs2533811446 · VCV1708378

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

ultra-rare (gnomAD MAF 2.89e-06)

Conditions

retinitis pigmentosa 14

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 3 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -3.7	GERP -2.4

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

Population frequency

dbSNP / gnomAD

Global frequency 0.000289% via dbSNP · ultra-rare

No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.

Variant & gene context

Gene: TULP1
Protein: p.Thr55fs
Coding: c.162dup
MANE Select: NM_003322
dbSNP: rs2533811446
Type: Duplication
Location: chr6:35512207 (GRCh38)
Gene constraint: LOEUF 1.019 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.10 · 2 PDB
Residue 55: the 'disordered' region

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

Disease context

retinitis pigmentosa 14 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Retinitis pigmentosa (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

TULP1 p.Gly270fs Likely pathogenic ★ same condition
TULP1 p.Ser152fs Pathogenic ★ same condition
TULP1 p.Tyr520fs Likely pathogenic ★ same condition
TULP1 p.Thr55Lys Uncertain significance ★ ⚠ same residue
TULP1 p.Thr55= Likely benign ★ same residue
TULP1 c.1495+1G>A Pathogenic/Likely pathogenic ★★ same condition
TULP1 c.1496-6C>A Pathogenic/Likely pathogenic ★★ same condition
TULP1 c.718+2T>C 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-thr55fs (accessed [today's date]).

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