CHRM1 p.Val300=
c.900G>A · VCV4912090
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0107%, afr)
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 2.7 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 7.235 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0107%
African / African-American · 8/74,636 alleles
Filtering AF
0.0053%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00382%
Overall
0.000623%
10/1,604,168 alleles · ultra-rare
exomes 4/1,451,898 · genomes 6/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0107% | 9,329 |
| Admixed American | 0.00341% | 29,359 |
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
- CHRM1
- Protein
- p.Val300=
- Coding
- c.900G>A
- MANE Select
- NM_000738
- Type
- single nucleotide variant
- Location
- chr11:62910201 (GRCh38)
- Gene constraint
- LOEUF 0.325 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.51 · 7 PDB
- Residue 300
- an α-helix
Similar variants
- CHRM1 p.Phe425Ser Likely pathogenic ★ same type
- CHRM1 p.Ala26Asp Uncertain significance ★ ⚠ same type
- CHRM1 p.Ala271Thr Uncertain significance ★ ⚠ same type
- CHRM1 p.Arg137Cys Uncertain significance ★ ⚠ same type
- CHRM1 p.Arg141Gln Uncertain significance ★ ⚠ same type
- CHRM1 p.Arg213Gln Uncertain significance ★ ⚠ same type
- CHRM1 p.Arg334His Uncertain significance ★ ⚠ same type
- CHRM1 p.Arg336Gln Uncertain significance ★ ⚠ 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/chrm1-p-val300 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown