CROCC p.Thr1968=
c.5904T>C · rs931140840 · VCV2638386
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0056%, nfe)
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 -9.6 | GERP -2.5 |
| Overall | ||
| CADD | 0.191 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0056%
European (non-Finnish) · 64/1,142,458 alleles
Filtering AF
0.00449%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00409%
Overall
0.00424%
65/1,532,110 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0056% | 17,851 |
| South Asian | 0.00119% | 83,730 |
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
- CROCC
- Protein
- p.Thr1968=
- Coding
- c.5904T>C
- MANE Select
- NM_014675
- dbSNP
- rs931140840
- Type
- single nucleotide variant
- Location
- chr1:16971584 (GRCh38)
- Gene constraint
- LOEUF 1.165 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.58 · 2 PDB
- Residue 1968
- the 'disordered' region
Similar variants
- CROCC p.Arg1094Trp Uncertain significance ★★ ⚠ same type
- CROCC p.Asp1119His Uncertain significance ★★ ⚠ same type
- CROCC p.Gly486Arg Uncertain significance ★★ ⚠ same type
- CROCC p.Arg1729Gln Likely benign ★★ same type
- CROCC p.Arg1908Cys Benign ★★ ⚠ same type
- CROCC p.Arg675His Benign ★★ same type
- CROCC p.Arg691His Benign ★★ same type
- CROCC p.Arg903Ser Benign/Likely 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/crocc-p-thr1968 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown