MAP3K7 c.607+2del
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
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. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| Splicing | ||
| Splice region | donor +2 | canonical splice dinucleotide (donor +2) · inside the BP7-excluded zone |
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 1.9, phastCons 1 |
| Non-coding constraint | Z -0.95 | 1 kb window · o/e 1.07 · regional · uncalibrated |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- MAP3K7
- Coding
- c.607+2del
- MANE Select
- NM_145331
- dbSNP
- rs1554184543
- Type
- Deletion
- Location
- chr6:90556498 (GRCh38)
- Gene constraint
- LOEUF 0.397 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 70.27 · 25 PDB
Similar variants
- MAP3K7 p.Arg155_Asp156delinsAsn Likely pathogenic ★ same type
- MAP3K7 p.His185_Thr187del Likely pathogenic ★ same type
- MAP3K7 c.120+8_120+27del Uncertain significance ★ same type
- MAP3K7 c.1291+4_1291+5del Uncertain significance ★ same type
- MAP3K7 p.Arg456_Pro460del Uncertain significance ★ same type
- MAP3K7 p.Glu66fs Uncertain significance ★ same type
- MAP3K7 c.121-109del Benign ★ same type
- MAP3K7 c.1210+299del 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/map3k7-c-607-plus-2del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown