CITED2 p.His26Asp
c.76C>G · VCV4083282
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.9516 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/3 damaging
AlphaMissense, REVEL, SaProt
Computational evidence
| Protein change | ||
| AlphaMissense | 0.9516 | likely pathogenic |
|---|---|---|
| REVEL | 0.217 | benign-leaning |
| SaProt | LLR -7.34 | tolerated |
| ⇒ AlphaMissense calls this damaging; REVEL and SaProt do not. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.4, phastCons 1 |
| Regional constraint | o/e 1.22 | unconstrained · MANE · 659 bp · p 8.7e-05 · regional, not allelic |
| Overall | ||
| CADD | 27.9 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CITED2
- Protein
- p.His26Asp
- Coding
- c.76C>G
- MANE Select
- NM_006079
- Type
- single nucleotide variant
- Location
- chr6:139373869 (GRCh38)
- Gene constraint
- LOEUF 0.588 · pLI 0.90 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 52.07 · 4 PDB
- Residue 26
- a UniProt-annotated variant site (found in a patient with myelomeningocele; uncertain significance)
Similar variants
- CITED2 p.Ala25Pro Uncertain significance ★★ ⚠ same type
- CITED2 p.Ala25Val Uncertain significance ★★ ⚠ same type
- CITED2 p.Pro128Ser Uncertain significance ★★ ⚠ same type
- CITED2 p.Ala7= Benign ★★ same type
- CITED2 p.Gly194= Benign/Likely benign ★★ same type
- CITED2 p.His160Leu Benign/Likely benign ★★ same type
- CITED2 p.His46= Likely benign ★★ same type
- CITED2 p.Pro209= 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/cited2-p-his26asp (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown