Is TCAP p.Ser157= (c.471C>T) pathogenic?

TCAP p.Ser157= (c.471C>T) is classified Likely benign in TCAP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-27). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with TCAP p.Ser157= (c.471C>T)?

TCAP p.Ser157= (c.471C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is TCAP p.Ser157= (c.471C>T) in the general population?

TCAP p.Ser157= (c.471C>T) is absent from gnomAD v4.1 (gnomAD).

TCAP p.Ser157=

c.471C>T · VCV3454001

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -1.4	GERP -5.3
Overall
CADD	7.359	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TCAP
Protein: p.Ser157=
Coding: c.471C>T
MANE Select: NM_003673
Type: single nucleotide variant
Location: chr17:39666076 (GRCh38)
Gene constraint: LOEUF 1.374 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.89 · 2 PDB
Residue 157: the 'disordered' region

Full TCAP 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

TCAP p.Ser157Thr Uncertain significance ★★ ⚠ same residue
TCAP p.Ser157Phe Uncertain significance ★ same residue
TCAP p.Gln53Ter Pathogenic/Likely pathogenic ★★ same condition
TCAP c.110+4A>G Uncertain significance ★★ same condition
TCAP p.Arg130His Uncertain significance ★★ ⚠ same condition
TCAP p.Arg153Ser Uncertain significance ★★ ⚠ same condition
TCAP p.Arg154Cys Uncertain significance ★★ ⚠ same condition
TCAP p.Arg154Ser 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/tcap-p-ser157 (accessed [today's date]).

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