Is TRIM2 p.Ser589= (c.1767C>T) pathogenic?

TRIM2 p.Ser589= (c.1767C>T) is classified Likely benign in TRIM2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-27). Ultra-rare (popmax 0.0508%, mid); Associated with Charcot-Marie-Tooth disease type 2R.

What condition is associated with TRIM2 p.Ser589= (c.1767C>T)?

TRIM2 p.Ser589= (c.1767C>T) is associated with Charcot-Marie-Tooth disease type 2R (ClinVar).

How common is TRIM2 p.Ser589= (c.1767C>T) in the general population?

TRIM2 p.Ser589= (c.1767C>T) is ultra-rare (popmax 0.0508%, mid) (gnomAD).

How is Charcot-Marie-Tooth disease type 2R inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

TRIM2 p.Ser589=

c.1767C>T · rs767007696 · VCV474605

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0508%, mid)

Conditions

Charcot-Marie-Tooth disease type 2R

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 -2.7	GERP -3.4
Overall
CADD	6.888	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0508% Middle Eastern · 3/5,910 alleles

Filtering AF 0.0138% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00736%

Overall 0.00147% 23/1,567,946 alleles · ultra-rare exomes 20/1,415,842 · genomes 3/152,104 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0508%	1,970
South Asian	0.00589%	16,990
Admixed American	0.002%	50,020
Remaining individualsnot grpmax-eligible	0.00166%	60,270
Finnishnot grpmax-eligible	0.00158%	63,228
African / African-American	0.00137%	72,892
European (non-Finnish)	0.00095%	105,317

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: TRIM2
Protein: p.Ser589=
Coding: c.1767C>T
MANE Select: NM_015271
dbSNP: rs767007696
Type: single nucleotide variant
Location: chr4:153315984 (GRCh38)
Gene constraint: LOEUF 0.398 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 84.91 · 6 PDB
Residue 589: a β-strand

Full TRIM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Charcot-Marie-Tooth disease type 2R — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Charcot-Marie-Tooth disease type 2R (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy

Similar variants

TRIM2 p.Ala139Val Uncertain significance ★★ ⚠ same condition
TRIM2 p.Ala174Thr Uncertain significance ★★ ⚠ same condition
TRIM2 p.Ala225Ser Uncertain significance ★★ ⚠ same condition
TRIM2 p.Ala225Thr Uncertain significance ★★ ⚠ same condition
TRIM2 p.Arg166Gln Uncertain significance ★★ ⚠ same condition
TRIM2 p.Arg166Trp Uncertain significance ★★ ⚠ same condition
TRIM2 p.Arg245His Uncertain significance ★★ ⚠ same condition
TRIM2 p.Arg321Gln 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/trim2-p-ser589 (accessed [today's date]).

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