CRYM p.Thr48=
c.144C>G · rs750687626 · VCV2715040
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0577%, 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 0.15 | GERP -1.6, phastCons 0.85 |
| Overall | ||
| CADD | 11.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0577%
Middle Eastern · 3/5,202 alleles
Filtering AF
0.0157%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00835%
Overall
0.00246%
38/1,547,812 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0577% | 1,734 |
| South Asian | 0.0131% | 7,637 |
| Remaining individualsnot grpmax-eligible | 0.00833% | 12,004 |
| European (non-Finnish) | 0.00157% | 63,723 |
| African / African-American | 0.00137% | 73,110 |
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
- CRYM
- Protein
- p.Thr48=
- Coding
- c.144C>G
- MANE Select
- NM_001376256
- dbSNP
- rs750687626
- Type
- single nucleotide variant
- Location
- chr16:21278108 (GRCh38)
- Gene constraint
- LOEUF 0.841 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.06 · 1 PDB
- Residue 48
- a β-strand
Similar variants
- CRYM p.Thr48Pro Uncertain significance ★ ⚠ same residue
- CRYM p.Ala178Glu Uncertain significance ★★ ⚠ same type
- CRYM p.Glu172Gly Uncertain significance ★★ ⚠ same type
- CRYM p.Leu72Val Uncertain significance ★★ ⚠ same type
- CRYM p.Met295Ile Uncertain significance ★★ ⚠ same type
- CRYM p.Thr95Ser Uncertain significance ★★ ⚠ same type
- CRYM p.Val4Leu Uncertain significance ★★ ⚠ same type
- CRYM c.171-118C>T Benign ★★ 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/crym-p-thr48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown