TCHH p.Arg629=
c.1887G>A · rs200947543 · VCV782911
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.32%, mid)
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 -2 | GERP -2.9 |
| Overall | ||
| CADD | 6.538 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.32%
Middle Eastern · 80/6,044 alleles
Filtering AF
1.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1%
Overall
0.814%
13,109/1,610,442 alleles · low-frequency
exomes 12,099/1,460,386 · genomes 1,010/150,056 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.32% | 76 |
| Ashkenazi Jewishnot grpmax-eligible | 1.24% | 81 |
| Finnishnot grpmax-eligible | 0.994% | 101 |
| European (non-Finnish) | 0.918% | 109 |
| Remaining individualsnot grpmax-eligible | 0.751% | 133 |
| Admixed American | 0.452% | 221 |
| Amishnot grpmax-eligible | 0.441% | 227 |
| South Asian | 0.376% | 266 |
| African / African-American | 0.171% | 584 |
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.Arg629=
- Coding
- c.1887G>A
- MANE Select
- NM_007113
- dbSNP
- rs200947543
- Type
- single nucleotide variant
- Location
- chr1:152111330 (GRCh38)
- Gene constraint
- LOEUF 1.811 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.96
- Residue 629
- the '9 x 28 aa approximate 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.Glu1601= Benign/Likely benign ★★ same type
- TCHH p.Glu430Gln Benign ★★ same type
- TCHH p.Glu650Lys Likely benign ★★ same type
- TCHH p.Glu675= 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-arg629 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown