--- title: "BRCA1 L1306X (c.3917del, rs886040175) | Dante Labs" description: "ClinVar classifies BRCA1 L1306X as Pathogenic (reviewed by expert panel). Where it sits in the genome, its predicted effect, and the Genome Test reports that look at it." url: "https://dantelabs.com/genes/brca1/variants/l1306x" --- 1. [Genes](https://dantelabs.com/genes) 2. [BRCA1](https://dantelabs.com/genes/brca1) 3. BRCA1 L1306X Variant # BRCA1 L1306X NM_007294.4(BRCA1):c.3917del (p.Leu1306Ter) Also known as - 4036delT - p.Leu1306Ter - p.L1306\* - rs886040175 * ClinVar classification Pathogenic * Review status 3 stars out of 4 reviewed by expert panel * Last evaluated 18 October 2016 * Expert panel Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.19-9814e911 Facts last changed 18 October 2026 ## Summary L1306X is a nonsense variant in BRCA1: it creates an early stop signal, so the protein the gene encodes is predicted to be cut short. ClinVar classifies it as pathogenic for breast-ovarian cancer, familial, susceptibility to, 1 (reviewed by expert panel). ## ClinVar classifications | Condition | Classification | Review status | Submissions | Last evaluated | | -------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------- | ----------------------------------------- | ------------ | --------------- | | breast-ovarian cancer, familial, susceptibility to, 1[ClinVar VCV000266417 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/266417/) | Pathogenic | 3 stars out of 4 reviewed by expert panel | 1 submission | 18 October 2016 | Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed. ## ACMG/AMP criteria The ACMG/AMP criteria L1306X meets, from its predicted effect in BRCA1, gnomAD and ClinVar. | Criterion | Strength | Rests on | | ------------------------------------------------------- | ----------- | ---------------------------------------------- | | PVS1 Null variant where loss of function causes disease | Very strong | stop_gained on NM_007294.4 | | PM2 Absent or very rare in population databases | Supporting | Not seen in gnomAD exomes, gnomAD genomes | | PP5 A reputable source reports it as pathogenic | Supporting | ClinVar: Pathogenic (reviewed by expert panel) | On these criteria alone: pathogenic. Assessed automatically, without functional, computational or family evidence. Not a clinical classification. ## Population frequency How often L1306X is seen among the people whose exomes and genomes gnomAD 4.1 brings together. | Dataset | Allele frequency | Allele count | Homozygotes | Commonest in | | -------------- | ---------------- | ------------ | ----------- | ------------ | | gnomAD exomes | Not seen | 0 of 0 | 0 | | | gnomAD genomes | Not seen | 0 of 0 | 0 | | Figures from gnomAD 4.1, as gnomAD publishes them. Groups are genetic ancestry groups as gnomAD infers them. They describe the variant in gnomAD's populations, not anyone's result. [L1306X in the gnomAD browser (opens in a new tab)](https://gnomad.broadinstitute.org/variant/17-43091613-CA-C?dataset=gnomad_r4) ## Where it lies in BRCA1 L1306X lies in exon 10 of the 23 in BRCA1's MANE Select transcript, NM_007294.4. [BRCA1 variants in exon 10 →](https://dantelabs.com/genes/brca1/variants?exon=10) [BRCA1's gene diagram →](https://dantelabs.com/genes/brca1#gene-structure) ## Molecular details | Gene | [BRCA1](https://dantelabs.com/genes/brca1) | | --------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- | | Transcript | NM_007294.4 MANE Select | | Coding DNA change (HGVS c.) | c.3917del | | Protein change (HGVS p.) | p.Leu1306Ter p.L1306\* | | Predicted consequence | Nonsense (stop gained) [stop_gained (opens in a new tab)](https://purl.obolibrary.org/obo/SO_0001587) | | Predicted impact | High | | Position (GRCh38) | chr17:43091613 CA>C | | Position (GRCh37) | chr17:41243630 CA>C | | dbSNP ID | [rs886040175 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs886040175) | | ClinVar Variation ID | [VCV000266417 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/266417/) | | ClinVar Allele ID | 261697 | | ClinGen Allele Registry ID | [CA10589714 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA10589714) | | ClinVar name | NM_007294.4(BRCA1):c.3917del (p.Asp1305_Leu1306insTer) | | Other names | 4036delT | ## BRCA1 L1306X in other databases - [ClinVar VCV000266417 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/266417/) - [dbSNP rs886040175 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs886040175) - [ClinGen Allele Registry CA10589714 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA10589714) - [gnomAD 17-43091613-CA-C (opens in a new tab)](https://gnomad.broadinstitute.org/variant/17-43091613-CA-C?dataset=gnomad_r4) - [Ensembl rs886040175 (opens in a new tab)](https://www.ensembl.org/Homo_sapiens/Variation/Explore?v=rs886040175) ## Reports that look at this variant (1) These Genome Test condition reports include L1306X among the variants they look at. | Report | Conditions | Inheritance | | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------- | ------------------ | | [Hereditary Breast and Ovarian Cancer (BRCA1/2)](https://dantelabs.com/conditions/hereditary-breast-ovarian-cancer) | Hereditary Breast and Ovarian Cancer Syndrome | Autosomal dominant | | | BRCA1-related cancer predisposition | Autosomal dominant | ## Other variants in BRCA1 - [A92Ffs\*4 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/brca1/variants/a92ffs4) - [A134Qfs\*7 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/brca1/variants/a134qfs7) - [A302Cfs\*2 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/brca1/variants/a302cfs2) - [A302Lfs\*12 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/brca1/variants/a302lfs12) - [A322Kfs\*2 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/brca1/variants/a322kfs2) - [A322Lfs\*19 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/brca1/variants/a322lfs19) - [A407Sfs\*5 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/brca1/variants/a407sfs5) - [A433Pfs\*8 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/brca1/variants/a433pfs8) - [A469Qfs\*6 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/brca1/variants/a469qfs6) - [A521X Pathogenic 3 stars out of 4](https://dantelabs.com/genes/brca1/variants/a521x) [All BRCA1 variants](https://dantelabs.com/genes/brca1/variants) ## Limitations This page describes publicly available information about a genetic variant. It is not a diagnosis, and it says nothing about whether you or anyone else carries this variant. Classifications come from ClinVar and change as new evidence is reviewed. A classification here may differ from the one in ClinVar today, or from the one a laboratory reports. Whole genome sequencing with short reads can miss or miscall some variants, particularly in repeated or highly similar stretches of DNA and in large insertions, deletions or rearrangements. If you have questions about a variant in your own results or in your family, talk to a genetic counsellor or your doctor. ## Sources & credits - Classifications from ClinVar (release 2026-10-12), National Center for Biotechnology Information. - Condition terms from the Mondo Disease Ontology (release 2026-10-06), used under CC BY 4.0. - Gene symbols and names from the HUGO Gene Nomenclature Committee (release 2026-10-16). - Allele identifiers from the ClinGen Allele Registry (release 2026-10-19-c4908f54). - Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information. - Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-19). - Difficult regions from the Genome in a Bottle Consortium (release v3.6). - Transcripts from MANE (release v1.5), NCBI and EMBL-EBI. - Predicted consequences from mehari (release 0.11.0), with transcript models from cdot. - Built from Dante Labs data release 2026.10.19-9814e911 of 19 October 2026. ## Cite this page APA > Dante Labs. (18 October 2026). BRCA1 L1306X (c.3917del, rs886040175) (Version 2026.10.19-9814e911). Retrieved 19 October 2026, from https\://dantelabs.com/genes/brca1/variants/l1306x Vancouver > Dante Labs. BRCA1 L1306X (c.3917del, rs886040175) \[Internet]. Version 2026.10.19-9814e911. 18 October 2026 \[cited 19 October 2026]. Available from: https\://dantelabs.com/genes/brca1/variants/l1306x Download citation [RIS](https://dantelabs.com/genes/brca1/variants/l1306x/cite.ris) [BibTeX](https://dantelabs.com/genes/brca1/variants/l1306x/cite.bib) [CSL-JSON](https://dantelabs.com/genes/brca1/variants/l1306x/cite.json) ## Read your whole genome From $449 Free shipping · Results in 6–8 weeks [Explore the Genome Test](https://dantelabs.com/whole-genome-sequencing)