Is TULP1 p.Lys261fs (c.780_783del) pathogenic?

TULP1 p.Lys261fs (c.780783del) is classified Pathogenic in TULP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-27). No gnomAD frequency available for this variant.

How common is TULP1 p.Lys261fs (c.780_783del) in the general population?

TULP1 p.Lys261fs (c.780_783del) is no gnomAD frequency available for this variant (gnomAD).

TULP1 p.Lys261fs

c.780_783del · rs2533802218 · VCV2747418

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 8 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.8	GERP 1.8, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: TULP1
Protein: p.Lys261fs
Coding: c.780_783del
MANE Select: NM_003322
dbSNP: rs2533802218
Type: Deletion
Location: chr6:35509248 (GRCh38)
Gene constraint: LOEUF 1.019 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.10 · 2 PDB
Residue 261: the 'disordered' region; a UniProt-annotated variant site (in); a UniProt-annotated variant site (in rp14)

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

Similar variants

TULP1 p.Lys261_Ser262delinsAsnArg Uncertain significance ★ same residue
TULP1 p.Lys261Asn Benign ★ same residue
TULP1 p.Arg419fs Pathogenic/Likely pathogenic ★★ same type
TULP1 p.Gln485fs Pathogenic/Likely pathogenic ★★ same type
TULP1 p.Leu504fs Pathogenic ★★ same type
TULP1 p.Lys274fs Pathogenic/Likely pathogenic ★★ same type
TULP1 p.Pro242fs Pathogenic ★★ same type
TULP1 p.Pro282fs Pathogenic ★★ 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/tulp1-p-lys261fs (accessed [today's date]).

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