SON p.Arg1970=
c.5910C>G · rs1458954705 · VCV2181311
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0118%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.031 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.24 | GERP -2.1, phastCons 0.53 |
| Overall | ||
| CADD | 2.033 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0118%
African / African-American · 8/67,858 alleles
Filtering AF
0.00585%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00425%
Overall
0.00142%
21/1,473,828 alleles · ultra-rare
exomes 14/1,326,538 · genomes 7/147,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0118% | 8,482 |
| Remaining individualsnot grpmax-eligible | 0.00177% | 56,360 |
| European (non-Finnish) | 0.00107% | 93,197 |
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
- SON
- Protein
- p.Arg1970=
- Coding
- c.5910C>G
- MANE Select
- NM_138927
- dbSNP
- rs1458954705
- Type
- single nucleotide variant
- Location
- chr21:33555141 (GRCh38)
- Gene constraint
- LOEUF 0.051 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.48 · 4 PDB
- Residue 1970
- the 'disordered' region; the '7 x 7 aa repeats of p-s-r-r-s-r-[ts]' region; the '2 x 19 aa repeats of p-s-r-r-r-r-s-r-s-v-v-r-r-r-s-f-s-i-s' region
Similar variants
- SON p.Arg1970Cys Uncertain significance ★ ⚠ same residue
- SON p.Arg1970His Uncertain significance ★ ⚠ same residue
- SON c.6321+1G>A Pathogenic ★★ same type
- SON p.Arg1081Ter Pathogenic ★★ same type
- SON p.Arg1112Ter Pathogenic ★★ same type
- SON p.Arg1825Ter Pathogenic ★★ same type
- SON p.Arg2008Ter Pathogenic ★★ same type
- SON p.Gln96Ter Pathogenic/Likely pathogenic ★★ 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/son-p-arg1970 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown