TCHH p.Arg1072=
c.3216G>A · VCV4872196
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00126%, sas)
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 -6.6 | GERP -2.1 |
| Overall | ||
| CADD | 2.839 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00126%
South Asian · 1/79,432 alleles
Overall
6.53e-05%
1/1,531,320 alleles · very rare
exomes 1/1,386,500 · genomes 0/144,820 · joint denominator
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
- TCHH
- Protein
- p.Arg1072=
- Coding
- c.3216G>A
- MANE Select
- NM_007113
- Type
- single nucleotide variant
- Location
- chr1:152110001 (GRCh38)
- Gene constraint
- LOEUF 1.811 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.96
- Residue 1072
- the '10 x 30 aa tandem repeats' region; the 'disordered' region
Similar variants
- TCHH p.Glu626Gly Uncertain significance ★★ ⚠ same type
- TCHH p.Ala686Gly Benign ★★ same type
- TCHH p.Arg1444Pro Likely benign ★★ ⚠ same type
- TCHH p.Arg1876Gln Likely benign ★★ same type
- TCHH p.Arg629= Benign/Likely benign ★★ same type
- TCHH p.Glu1601= Benign/Likely benign ★★ same type
- TCHH p.Glu430Gln Benign ★★ same type
- TCHH p.Glu650Lys Likely benign ★★ same type
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/tchh-p-arg1072 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown