Is TBCE p.Asp430= (c.1290T>C) pathogenic?

TBCE p.Asp430= (c.1290T>C) is classified Likely benign in TBCE (ClinVar, Single submitter, 1 submitter; last evaluated 2018-03-29). Very rare (popmax 0.00223%, eas).

How common is TBCE p.Asp430= (c.1290T>C) in the general population?

TBCE p.Asp430= (c.1290T>C) is very rare (popmax 0.00223%, eas) (gnomAD).

TBCE p.Asp430=

c.1290T>C · rs1415511790 · VCV737370

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

⚠ 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.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -5.4	GERP -3.7
Overall
CADD	4.483	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,858 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.00031% 5/1,613,972 alleles · very rare exomes 5/1,461,770 · genomes 0/152,202 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,858
South Asian	0.0011%	91,074
European (non-Finnish)	0.000254%	393,317

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: TBCE
Protein: p.Asp430=
Coding: c.1290T>C
MANE Select: NM_003193
dbSNP: rs1415511790
Type: single nucleotide variant
Location: chr1:235441833 (GRCh38)

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

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/tbce-p-asp430 (accessed [today's date]).

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