Variant
RPGR L460Ifs*2
NM_001034853.2(RPGR):c.1377_1378del (p.Leu460IlefsTer2)
- p.Leu460IlefsTer2
- p.L460Ifs*2
- rs62653029
- ClinVar classification
- Pathogenic
- Review status
- 3 stars out of 4reviewed by expert panel
- Last evaluated
- 25 January 2026
- Expert panel
- ClinGen X-linked Inherited Retinal Disease Variant Curation Expert Panel, ClinGen
Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.16-c6eea6bfFacts last changed 16 October 2026
Reference genomeGRCh38hg38
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Summary
L460Ifs*2 is a frameshift variant in RPGR: it adds or removes DNA letters in a way that shifts how the rest of the gene's code is read. ClinVar classifies it as pathogenic for RPGR-Related Retinopathy (reviewed by expert panel).
ClinVar classifications
| Condition | Classification | Review status | Submissions | Last evaluated |
|---|---|---|---|---|
| RPGR-Related RetinopathyClinVar VCV000098739 (opens in a new tab) | Pathogenic | 3 stars out of 4reviewed by expert panel | 1 submission | 25 January 2026 |
Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed.
Where it lies in RPGR
L460Ifs*2 lies in exon 11 of the 15 in RPGR's MANE Select transcript, NM_001034853.2.
Molecular details
| Gene | RPGR |
|---|---|
| Transcript | NM_001034853.2MANE Select |
| Coding DNA change (HGVS c.) | c.1377_1378del |
| Protein change (HGVS p.) | p.Leu460IlefsTer2p.L460Ifs*2 |
| Predicted consequence | Frameshiftframeshift_variant (opens in a new tab)frameshift_truncation (opens in a new tab) |
| Predicted impact | High |
| Position (GRCh38) | chrX:38297319 AAG>A |
| Position (GRCh37) | chrX:38156572 AAG>A |
| dbSNP ID | rs62653029 (opens in a new tab) |
| ClinVar Variation ID | VCV000098739 (opens in a new tab) |
| ClinVar Allele ID | 104629 |
| ClinGen Allele Registry ID | CA226358 (opens in a new tab) |
| ClinVar name | NM_001034853.2(RPGR):c.1377_1378del (p.Leu460fs) |
RPGR L460Ifs*2 in other databases
Reports that look at this variant (1)
These Genome Test condition reports include L460Ifs*2 among the variants they look at.
| Report | Conditions | Inheritance |
|---|---|---|
| Retinitis Pigmentosa | RPGR-Related Retinopathy | X-linked recessive |
Other variants in RPGR
- A308PLikely pathogenic3 stars out of 4
- A365Cfs*12Pathogenic3 stars out of 4
- A781Rfs*34Pathogenic3 stars out of 4
- c.28+1G>APathogenic3 stars out of 4
- c.28+1G>CPathogenic3 stars out of 4
- c.28+2T>CPathogenic3 stars out of 4
- c.28+2T>GPathogenic3 stars out of 4
- c.29-2A>GPathogenic3 stars out of 4
- c.154+1G>APathogenic3 stars out of 4
- c.154+3_154+6delPathogenic3 stars out of 4
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 2026-10-16-c4908f54).
- Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information.
- Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-16).
- 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 2026.10.16-c6eea6bf of 16 October 2026.
Cite this page
Dante Labs. (16 October 2026). RPGR L460Ifs*2 (c.1377_1378del, rs62653029) (Version 2026.10.16-c6eea6bf). Retrieved 16 October 2026, from https://dantelabs.com/genes/rpgr/variants/l460ifs2
Dante Labs. RPGR L460Ifs*2 (c.1377_1378del, rs62653029) [Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 [cited 16 October 2026]. Available from: https://dantelabs.com/genes/rpgr/variants/l460ifs2
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