Is TNNT2 p.Phe258= (c.774C>T) pathogenic?

TNNT2 p.Phe258= (c.774C>T) is classified Likely benign in TNNT2 (ClinVar, Multiple submitters, 12 submitters; last evaluated 2026-05-01). Very rare (popmax 0.00983%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with TNNT2 p.Phe258= (c.774C>T)?

TNNT2 p.Phe258= (c.774C>T) is associated with Cardiovascular phenotype, cardiomyopathy, hypertrophic cardiomyopathy 2 (ClinVar).

How common is TNNT2 p.Phe258= (c.774C>T) in the general population?

TNNT2 p.Phe258= (c.774C>T) is very rare (popmax 0.00983%, nfe) (gnomAD).

TNNT2 p.Phe258=

c.774C>T · rs397516481 · VCV43668

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 12 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00983%, nfe)

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 -4.4	GERP -3.9
Overall
CADD	9.758	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00983% European (non-Finnish) · 116/1,179,992 alleles

Filtering AF 0.00834% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00776%

Overall 0.00762% 123/1,614,110 alleles · very rare exomes 110/1,461,862 · genomes 13/152,248 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00983%	10,172
Remaining individualsnot grpmax-eligible	0.008%	12,500
Admixed American	0.00167%	60,022
African / African-American	0.00133%	75,016

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: TNNT2
Protein: p.Phe258=
Coding: c.774C>T
MANE Select: NM_001276345
dbSNP: rs397516481
Type: single nucleotide variant
Location: chr1:201361315 (GRCh38)
Gene constraint: LOEUF 0.683 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 78.93 · 25 PDB
Residue 258: an α-helix

Full TNNT2 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

Also linked: cardiomyopathy hypertrophic cardiomyopathy 2 dilated cardiomyopathy 1D cardiomyopathy, familial restrictive, 3

Similar variants

TNNT2 p.Phe258Leu Uncertain significance ★★ ⚠ same residue
TNNT2 p.Phe258Val Uncertain significance ★★ ⚠ same residue
TNNT2 p.Phe258Tyr Uncertain significance ★ ⚠ same residue
TNNT2 c.851+1G>A Likely pathogenic ★★★ same condition
TNNT2 p.Arg104His Likely pathogenic ★★★ same condition
TNNT2 p.Trp297Ter Likely pathogenic ★★★ same condition
TNNT2 p.Arg296Cys Uncertain significance ★★★ ⚠ same condition
TNNT2 p.Arg288Cys Likely benign ★★★ 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/tnnt2-p-phe258 (accessed [today's date]).

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