SRPRB p.Val105=
c.315C>T · rs112398870 · VCV785065
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.45%, 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 1, phastCons 1 |
| Overall | ||
| CADD | 12.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.45%
African / African-American · 3,328/74,796 alleles
Filtering AF
4.32%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.27%
Overall
0.244%
3,923/1,609,990 alleles · low-frequency
exomes 2,008/1,457,792 · genomes 1,915/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.45% | 22 |
| Admixed American | 0.345% | 290 |
| Remaining individualsnot grpmax-eligible | 0.343% | 291 |
| Middle Eastern | 0.297% | 337 |
| Ashkenazi Jewishnot grpmax-eligible | 0.071% | 1,408 |
| South Asian | 0.0144% | 6,935 |
| European (non-Finnish) | 0.0108% | 9,283 |
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
- SRPRB
- Protein
- p.Val105=
- Coding
- c.315C>T
- MANE Select
- NM_001379313
- dbSNP
- rs112398870
- Type
- single nucleotide variant
- Location
- chr3:133807811 (GRCh38)
- Gene constraint
- LOEUF 1.05 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.30 · 1 PDB
Similar variants
- SRPRB p.Ala211Val Uncertain significance ★ ⚠ same type
- SRPRB p.Arg109Lys Uncertain significance ★ ⚠ same type
- SRPRB p.Arg150Gln Uncertain significance ★ ⚠ same type
- SRPRB p.Arg208His Uncertain significance ★ ⚠ same type
- SRPRB p.Arg58Gln Uncertain significance ★ ⚠ same type
- SRPRB p.Asn106Ser Uncertain significance ★ ⚠ same type
- SRPRB p.Asn171Ser Uncertain significance ★ ⚠ same type
- SRPRB p.Asn171Thr 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/srprb-p-val105 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown