Is TCTN3 p.Pro76= (c.228T>G) pathogenic?

TCTN3 p.Pro76= (c.228T>G) is classified Likely benign in TCTN3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-09). Absent from gnomAD v4.1; Associated with Joubert syndrome 18.

What condition is associated with TCTN3 p.Pro76= (c.228T>G)?

TCTN3 p.Pro76= (c.228T>G) is associated with Joubert syndrome 18, orofaciodigital syndrome IV (ClinVar).

How common is TCTN3 p.Pro76= (c.228T>G) in the general population?

TCTN3 p.Pro76= (c.228T>G) is absent from gnomAD v4.1 (gnomAD).

TCTN3 p.Pro76=

c.228T>G · rs1468519329 · VCV2950554

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Joubert syndrome 18

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.017	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.5	GERP -3.1
Overall
CADD	5.238	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TCTN3
Protein: p.Pro76=
Coding: c.228T>G
MANE Select: NM_015631
dbSNP: rs1468519329
Type: single nucleotide variant
Location: chr10:95693672 (GRCh38)

Full TCTN3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Joubert syndrome 18 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: orofaciodigital syndrome IV

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/tctn3-p-pro76 (accessed [today's date]).

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