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Gene

PRPF31

pre-mRNA processing factor 31

Summary

Cytogenetic location
19q13.42
Coordinates
Chromosome 19: 54,115,754–54,131,713 (GRCh38)
Exons
14 exons across 16 kb
Protein
499 amino acids
Inheritance
Autosomal dominant
Also known as
NY-BR-99, PRP31, hPrp31, SNRNP61
Previous symbols
RP11
MANE Select transcript
ENST00000321030.9NM_015629.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Retinitis Pigmentosa

    • PRPF31-Related RetinopathyAutosomal dominant

      A retinal dystrophy caused by changes in the PRPF31 gene.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong

    • One of 77 genes linked to it

      A group of inherited retinal dystrophies with progressive loss of rod and then cone photoreceptors, causing night blindness and gradual loss of peripheral vision.

      • 4 GenCC submitters rate it definitive or strong

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How PRPF31 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 19, with a bracket where PRPF31 sits. PRPF31 and 33 genes near it on chromosome 19, from 53,623,734 to 54,623,733.Chromosome 1919q13.42p13.3p13.2p13.13p13.12p13.11p12p11q11q12q13.11q13.12q13.13q13.2q13.31q13.32q13.33q13.41q13.42q13.4353.8 Mb54 Mb54.2 Mb54.4 Mb54.6 MbDPRX: 53,600,777–53,637,014, forward strandDPRXNLRP12: 53,792,139–53,824,403, reverse strandNLRP12MYADM: 53,864,763–53,878,125, forward strandMYADMPRKCG: 53,879,190–53,907,652, forward strandPRKCGCACNG7: 53,909,264–53,943,950, forward strandCACNG7CACNG8: 53,962,937–53,990,215, forward strandCACNG8CACNG6: 53,991,605–54,012,670, forward strandCACNG6VSTM1: 54,040,825–54,063,959, reverse strandVSTM1TARM1: 54,069,895–54,081,365, reverse strandOSCAR: 54,094,668–54,102,692, reverse strandNDUFA3: 54,102,728–54,111,522, forward strandNDUFA3TFPT: 54,107,015–54,115,666, reverse strandTFPTPRPF31: 54,115,754–54,131,713, forward strandPRPF31CNOT3: 54,137,710–54,155,708, forward strandCNOT3LENG1: 54,155,161–54,159,760, reverse strandTMC4: 54,160,095–54,173,250, reverse strandTMC4MBOAT7: 54,173,412–54,189,882, reverse strandMBOAT7TSEN34: 54,188,464–54,194,538, forward strandRPS9: 54,200,466–54,249,003, forward strandRPS9LILRB3: 54,215,940–54,223,506, reverse strandLILRB3LILRA6: 54,236,590–54,242,820, reverse strandLILRA6LILRB5: 54,249,421–54,257,339, reverse strandLILRB5LILRB2: 54,273,812–54,281,184, reverse strandLILRA5: 54,307,037–54,313,177, reverse strandLILRA5LILRA4: 54,333,185–54,339,162, reverse strandLILRA4LAIR1: 54,351,384–54,370,558, reverse strandLAIR1TTYH1: 54,415,219–54,436,904, forward strandTTYH1LENG8: 54,449,157–54,462,022, forward strandLENG8LENG9: 54,461,732–54,463,778, reverse strandLENG9CDC42EP5: 54,465,026–54,473,316, reverse strandCDC42EP5LAIR2: 54,497,879–54,510,694, forward strandLAIR2LILRA2: 54,572,920–54,590,287, forward strandLILRA2LILRA1: 54,593,582–54,603,259, forward strandLILRA1LILRB1: 54,616,309–54,638,022, forward strandLILRB1Diagram of PRPF31: 14 exons on the forward strand of chromosome 19Exon 2: 13 known disease-causing sitesExon 3: 4 known disease-causing sitesExon 4: 6 known disease-causing sitesExon 5: 4 known disease-causing sitesExon 6: 3 known disease-causing sitesExon 7: 9 known disease-causing sitesExon 8: 5 known disease-causing sitesExon 9: 8 known disease-causing sitesExon 10: 9 known disease-causing sitesExon 11: 6 known disease-causing sitesExon 12: 5 known disease-causing sitesExon 13: 1 known disease-causing siteExon 1: 54,115,754–54,115,797, 44 basesExon 2: 54,118,271–54,118,455, 185 basesExon 3: 54,118,573–54,118,633, 61 basesExon 4: 54,121,860–54,121,943, 84 basesExon 5: 54,122,497–54,122,594, 98 basesExon 6: 54,123,454–54,123,560, 107 basesExon 7: 54,123,749–54,123,918, 170 basesExon 8: 54,124,499–54,124,656, 158 basesExon 9: 54,126,528–54,126,617, 90 basesExon 10: 54,128,073–54,128,200, 128 basesExon 11: 54,128,305–54,128,377, 73 basesExon 12: 54,129,057–54,129,185, 129 basesExon 13: 54,129,272–54,129,370, 99 basesExon 14: 54,131,307–54,131,713, 407 bases124681012145′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 1.8 kb of the gene's 16 kb; 1,500 of those bases code for the protein.

How a genome test reads PRPF31

98

positions in PRPF31 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 16 kb of PRPF31, introns included, not only the 1.8 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). PRPF31 gene: pre-mRNA processing factor 31. Retrieved 17 October 2026, from https://dantelabs.com/genes/prpf31

Vancouver

Dante Labs. PRPF31 gene: pre-mRNA processing factor 31 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/prpf31

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