Is TULP1 p.124DEE[1] (c.369GGACGAGGA[1]) pathogenic?

TULP1 p.124DEE[1] (c.369GGACGAGGA[1]) is classified Conflicting classifications of pathogenicity in TULP1 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-01-20). Ultra-rare (popmax 0.0333%, mid).

How common is TULP1 p.124DEE[1] (c.369GGACGAGGA[1]) in the general population?

TULP1 p.124DEE[1] (c.369GGACGAGGA[1]) is ultra-rare (popmax 0.0333%, mid) (gnomAD).

TULP1 p.124DEE[1]

c.369GGACGAGGA[1] · rs758969883 · VCV968043

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0333%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.061	GERP -0.58, phastCons 0.027
Overall
CADD	10.75	PHRED · no single calibrated threshold — expert panels disagree
Region caveats
Repeat context	tandem	(CCT)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0333% Middle Eastern · 2/6,010 alleles

Filtering AF 0.0155% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0129%

Overall 0.00437% 70/1,603,002 alleles · ultra-rare exomes 55/1,451,620 · genomes 15/151,382 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0333%	3,005
African / African-American	0.0241%	4,153
Remaining individualsnot grpmax-eligible	0.0113%	8,860
South Asian	0.0044%	22,750
European (non-Finnish)	0.00315%	31,727
Admixed American	0.00168%	59,496
Finnishnot grpmax-eligible	0.00165%	60,728

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.124DEE[1]
Coding: c.369GGACGAGGA[1]
MANE Select: NM_003322
dbSNP: rs758969883
Type: Microsatellite
Location: chr6:35510974 (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

Similar variants

TULP1 c.360_362delGGA Uncertain significance ★★ same type
TULP1 p.124DEE[3] Uncertain significance ★★ same type
TULP1 p.Lys138fs Likely pathogenic ★ same type
TULP1 p.Asn463del Uncertain significance ★ same type
TULP1 p.Glu254del Conflicting classifications of pathogenicity ★ same type
TULP1 c.499+13_499+21del Likely benign ★ 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-124dee-1 (accessed [today's date]).

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