CHD3 p.Ala1979Lys
c.5935_5936delinsAA · rs2545197283 · VCV2501826
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 0.4, phastCons 1 |
| Regional constraint | o/e 0.85 | unconstrained · MANE · 1,019 bp · p 0.084 · regional, not allelic |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CHD3
- Protein
- p.Ala1979Lys
- Coding
- c.5935_5936delinsAA
- MANE Select
- NM_001005273
- dbSNP
- rs2545197283
- Type
- Indel
- Location
- chr17:7911517 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 1979
- a UniProt-annotated variant site (in snibcps)
Similar variants
- CHD3 c.4073-3delinsAA Pathogenic ★ same type
- CHD3 p.Asn1359_Gln1360delinsLysTrpGlyTrpSer Likely pathogenic ★ same type
- CHD3 p.Asp1120His Likely pathogenic ★ same type
- CHD3 p.Pro538fs Pathogenic ★ same type
- CHD3 p.Ala1933_Ser1936delinsGluGly Uncertain significance ★ same type
- CHD3 p.Gly1941Ala Uncertain significance ★ same type
- CHD3 p.Lys627_Pro628delinsAsnSer Uncertain significance ★ same type
- CHD3 p.Phe73delinsLeuPro 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/chd3-p-ala1979lys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown