TECRL p.Pro45=
c.135T>A · rs1189197462 · VCV1770814
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, amr)
Conditions
1
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 1.1 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 2.915 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,908 alleles
Filtering AF
0.000554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000186%
3/1,610,272 alleles · very rare
exomes 3/1,458,198 · genomes 0/152,074 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00334% | 29,954 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,238 |
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
- TECRL
- Protein
- p.Pro45=
- Coding
- c.135T>A
- MANE Select
- NM_001010874
- dbSNP
- rs1189197462
- Type
- single nucleotide variant
- Location
- chr4:64409217 (GRCh38)
- Gene constraint
- LOEUF 1.563 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.32
Similar variants
- TECRL p.Pro45Ser Benign/Likely benign ★★ same residue
- TECRL c.730+1G>A Likely pathogenic ★★ same condition
- TECRL p.Arg196Ter Pathogenic/Likely pathogenic ★★ same condition
- TECRL p.Cys189Ter Pathogenic ★★ same condition
- TECRL p.Gln68Ter Pathogenic/Likely pathogenic ★★ same condition
- TECRL p.Trp225Ter Pathogenic ★★ same condition
- TECRL c.234+5G>A Uncertain significance ★★ same condition
- TECRL c.774+3A>G 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/tecrl-p-pro45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown