CSN2 p.His51=
c.153C>T · rs150033877 · VCV2654792
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.36%, mid)
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 3.5 | GERP 0.99, phastCons 1 |
| Overall | ||
| CADD | 2.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.36%
Middle Eastern · 82/6,040 alleles
Filtering AF
1.12%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.03%
Overall
0.101%
1,623/1,611,658 alleles · low-frequency
exomes 1,480/1,459,424 · genomes 143/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.36% | 74 |
| Remaining individualsnot grpmax-eligible | 0.202% | 495 |
| Admixed American | 0.145% | 687 |
| Ashkenazi Jewishnot grpmax-eligible | 0.102% | 984 |
| European (non-Finnish) | 0.0995% | 1,005 |
| South Asian | 0.0858% | 1,165 |
| African / African-American | 0.0614% | 1,629 |
| Finnishnot grpmax-eligible | 0.00313% | 31,957 |
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
- CSN2
- Protein
- p.His51=
- Coding
- c.153C>T
- MANE Select
- NM_001891
- dbSNP
- rs150033877
- Type
- single nucleotide variant
- Location
- chr4:69957796 (GRCh38)
- Gene constraint
- LOEUF 1.168 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.09
Similar variants
- CSN2 p.His51Arg Likely benign ★ same residue
- CSN2 p.Ala162Thr Uncertain significance ★ ⚠ same type
- CSN2 p.Ala190Gly Uncertain significance ★ ⚠ same type
- CSN2 p.Ala85Pro Uncertain significance ★ ⚠ same type
- CSN2 p.Arg189Lys Uncertain significance ★ ⚠ same type
- CSN2 p.Asp106Asn Uncertain significance ★ ⚠ same type
- CSN2 p.Gln194Arg Uncertain significance ★ ⚠ same type
- CSN2 p.Glu20Asp 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/csn2-p-his51 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown