CLVS1 p.Asn147=
c.441T>C · VCV3834257
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0135%, nfe)
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 1.2 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 15.76 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0135%
European (non-Finnish) · 159/1,179,738 alleles
Filtering AF
0.0117%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0111%
Overall
0.0113%
182/1,613,528 alleles · ultra-rare
exomes 167/1,461,230 · genomes 15/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0135% | 7,420 |
| Finnishnot grpmax-eligible | 0.0125% | 7,996 |
| South Asian | 0.00879% | 11,375 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,495 |
| Admixed American | 0.00167% | 59,948 |
| African / African-American | 0.00133% | 75,008 |
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
- CLVS1
- Protein
- p.Asn147=
- Coding
- c.441T>C
- MANE Select
- NM_173519
- Type
- single nucleotide variant
- Location
- chr8:61300268 (GRCh38)
- Gene constraint
- LOEUF 0.473 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 82.01
- Residue 147
- the cral-trio domain
Similar variants
- CLVS1 p.Ala28Ser Uncertain significance ★ ⚠ same type
- CLVS1 p.Arg39Cys Uncertain significance ★ ⚠ same type
- CLVS1 p.Asn153Asp Uncertain significance ★ ⚠ same type
- CLVS1 p.Asn178Ser Uncertain significance ★ ⚠ same type
- CLVS1 p.Asn224Ser Uncertain significance ★ ⚠ same type
- CLVS1 p.Asn346Thr Uncertain significance ★ ⚠ same type
- CLVS1 p.Asp106Asn Uncertain significance ★ ⚠ same type
- CLVS1 p.Asp114Asn 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/clvs1-p-asn147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown