Is TNXB p.Thr1663= (c.4989G>A) pathogenic?

TNXB p.Thr1663= (c.4989G>A) is classified Likely benign in TNXB (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-20). Very rare (popmax 0.00228%, sas); Associated with Cardiovascular phenotype.

What condition is associated with TNXB p.Thr1663= (c.4989G>A)?

TNXB p.Thr1663= (c.4989G>A) is associated with Cardiovascular phenotype (ClinVar).

How common is TNXB p.Thr1663= (c.4989G>A) in the general population?

TNXB p.Thr1663= (c.4989G>A) is very rare (popmax 0.00228%, sas) (gnomAD).

TNXB p.Thr1663=

c.4989G>A · rs745926021 · VCV2451162

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00228%, sas)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.4	GERP -3.8
Overall
CADD	0.614	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00228% South Asian · 2/87,738 alleles

Filtering AF 0.000378% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000142%

Overall 0.000502% 8/1,592,954 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00228%	43,869
Admixed American	0.00169%	59,294
Remaining individualsnot grpmax-eligible	0.00162%	61,608
European (non-Finnish)	0.000343%	291,969

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: TNXB
Protein: p.Thr1663=
Coding: c.4989G>A
MANE Select: NM_001365276
dbSNP: rs745926021
Type: single nucleotide variant
Location: chr6:32071991 (GRCh38)
Gene constraint: LOEUF 0.674 · pLI <0.01 (gnomAD)
Residue 1663: the fibronectin type-iii 9 domain

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TNXB p.Thr1663Met Uncertain significance ★★ same residue
TNXB p.Arg821Ter Pathogenic/Likely pathogenic ★★ same condition
TNXB c.403+3G>A Uncertain significance ★★ same condition
TNXB c.4990+3G>A Uncertain significance ★★ same condition
TNXB c.9757+4A>G Uncertain significance ★★ same condition
TNXB p.Ala1231Val Uncertain significance ★★ ⚠ same condition
TNXB p.Ala1571Thr Uncertain significance ★★ ⚠ same condition
TNXB p.Ala1860Thr Uncertain significance ★★ ⚠ 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/tnxb-p-thr1663 (accessed [today's date]).

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