Gene Callability Atlas

Know where your
genetic test can't see.

Search over 5,000 medically relevant genes for their sequencing blind spots — down to the exon, across GRCh38 and T2T-CHM13, with the evidence behind every flag.

Try:
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Gene not in demo dataset

The production platform covers 464+ genes with significant NGS challenges, derived from the Mandelker et al. 2016 dead-zone catalog and Blindspot's internal GIAB and liftover analysis. Request access to search the full evidence base.

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ⓘDemo data — a curated subset of the Blindspot database. Exon models from RefSeq Select; difficult-region overlap and intervals from GIAB v3.6 stratification; category flags from the reference-assembly comparison; gene validity from ClinGen. Every figure is traceable to a documented source.
What we found
1 in 7pathogenic variants is technically challenging to detect by standard NGS (Lincoln et al. 2021, n=450,000)
34.3%of Mendelian families encounter at least one diagnostic challenge from sequencing (AlAbdi et al. 2023, n=4,577)
99.3%of medically relevant genes touch a difficult region in GRCh38 — but the actionable blind spots are a specific, knowable subset
46.9%of medically relevant genes have at least one ClinVar variant that fails liftover from GRCh38 to T2T-CHM13
487medically relevant genes with NGS dead zones
239P/LP variants absent from T2T-CHM13
The platform

One search. The whole picture.

Every gene resolves to the exon, across GRCh38 and T2T-CHM13, with the peer-reviewed evidence behind each flag — the same layout for every gene, driven by the same validated data.

Exon-level resolution
Real RefSeq Select transcript structure overlaid on GIAB difficult regions — see which exons sit in a segmental duplication, not just a gene-level percentage.
Three-assembly comparison
GRCh38, T2T-CHM13, and legacy GRCh37 side by side — because a gene that looks clean on one reference can be a blind spot on another.
Mechanism, not just a flag
Each blind spot explains its mechanism, clinical consequence, and the orthogonal approaches labs commonly use — traced to the primary literature.
ClinGen gene validity
Curated gene–disease relationships with classifications and modes of inheritance — including refuted associations that shouldn't be on a panel.
Early access

Ready to see the blind spots
in your panel?

Blindspot Genetics is in early access for ordering physicians, clinical labs, and genetic counselors.

The evidence base →
Blindspot Genetics is an informational and educational reference tool. It surfaces published, gene- and assembly-level sequencing limitations to support test selection and clinical understanding. It does not provide medical advice, make patient-specific recommendations, or replace confirmatory testing, laboratory judgment, or genetic counseling. Clinical decisions remain the responsibility of the ordering provider and testing laboratory. Every figure is traceable to peer-reviewed literature or a documented internal pipeline.