SORD p.Pro124=
c.372C>T · rs151103932 · VCV1012844
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0453%, 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 -20 | GERP -3.7 |
| Overall | ||
| CADD | 0.041 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0453%
African / African-American · 34/74,980 alleles
Filtering AF
0.0333%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0292%
Overall
0.0267%
430/1,612,940 alleles · ultra-rare
exomes 357/1,460,672 · genomes 73/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0453% | 2,205 |
| South Asian | 0.0407% | 2,460 |
| Finnishnot grpmax-eligible | 0.0359% | 2,783 |
| Remaining individualsnot grpmax-eligible | 0.0352% | 2,840 |
| European (non-Finnish) | 0.0254% | 3,943 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.0133% | 7,502 |
| East Asian | 0.0111% | 8,973 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
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
- SORD
- Protein
- p.Pro124=
- Coding
- c.372C>T
- MANE Select
- NM_003104
- dbSNP
- rs151103932
- Type
- single nucleotide variant
- Location
- chr15:45061173 (GRCh38)
- Gene constraint
- LOEUF 0.929 · pLI 0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 98.06 · 3 PDB
- Residue 124
- a UniProt-annotated variant site (in hmnr8)
Similar variants
- SORD p.Ala153Asp Pathogenic/Likely pathogenic ★★ same type
- SORD p.Ala259Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- XDH c.1602+1G>A Likely pathogenic ★★ same type
- XDH c.565-1G>A Likely pathogenic ★★ same type
- XDH p.Arg1283Ter Pathogenic ★★ same type
- XDH p.Arg228Ter Pathogenic/Likely pathogenic ★★ same type
- XDH p.Arg825Ter Pathogenic/Likely pathogenic ★★ same type
- XDH p.Gln251Ter 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/sord-p-pro124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown