Is TCAP p.Pro142fs (c.425_426del) pathogenic?

TCAP p.Pro142fs (c.425426del) is classified Uncertain significance in TCAP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-24). No gnomAD frequency available for this variant; Associated with hypertrophic cardiomyopathy 25.

What condition is associated with TCAP p.Pro142fs (c.425_426del)?

TCAP p.Pro142fs (c.425_426del) is associated with hypertrophic cardiomyopathy 25, familial hypertrophic cardiomyopathy (ClinVar).

How common is TCAP p.Pro142fs (c.425_426del) in the general population?

TCAP p.Pro142fs (c.425_426del) is no gnomAD frequency available for this variant (gnomAD).

TCAP p.Pro142fs

c.425_426del · rs2145074542 · VCV1521328

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hypertrophic cardiomyopathy 25

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (2 of 2) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6	GERP 2.6, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: TCAP
Protein: p.Pro142fs
Coding: c.425_426del
MANE Select: NM_003673
dbSNP: rs2145074542
Type: Deletion
Location: chr17:39666030 (GRCh38)
Gene constraint: LOEUF 1.374 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.89 · 2 PDB

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

Disease context

hypertrophic cardiomyopathy 25 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: familial hypertrophic cardiomyopathy

Similar variants

TCAP p.Pro142Thr Uncertain significance ★ ⚠ same residue
TCAP p.Pro142= Likely benign ★ same residue
TCAP c.110_110+1del Pathogenic ★★ same condition
TCAP p.Ile111fs Uncertain significance ★★ same condition
TCAP p.Phe21del Uncertain significance ★★ same condition
TCAP p.Gln46fs Pathogenic ★ same condition
TCAP p.Glu12fs Pathogenic ★ same condition
TCAP p.Tyr51fs Pathogenic ★ 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/tcap-p-pro142fs (accessed [today's date]).

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