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Gene

PRPF3

pre-mRNA processing factor 3

Summary

Cytogenetic location
1q21.2
Coordinates
Chromosome 1: 150,321,533–150,353,233 (GRCh38)
Exons
16 exons across 31.7 kb
Protein
683 amino acids
Also known as
Prp3, hPrp3, SNRNP90
Previous symbols
RP18
MANE Select transcript
ENST00000324862.7NM_004698.4
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

      • 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.

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

    How PRPF3 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 1, with a bracket where PRPF3 sits. PRPF3 and 33 genes near it on chromosome 1, from 149,837,383 to 150,837,382.Chromosome 11q21.2p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q44150 Mb150.2 Mb150.4 Mb150.6 Mb150.8 MbH4C14: 149,832,657–149,839,767, forward strandH3C14: 149,840,687–149,841,208, reverse strandH3C14H2AC18: 149,842,218–149,842,750, reverse strandH2AC18H2AC19: 149,851,061–149,851,652, forward strandH3C15: 149,852,608–149,853,125, forward strandH3C15H4C15: 149,854,045–149,861,159, reverse strandH2BC21: 149,884,459–149,886,682, reverse strandBOLA1: 149,886,406–149,900,798, forward strandBOLA1H2AC20: 149,886,918–149,887,411, forward strandH2AC21: 149,887,469–149,887,965, reverse strandSV2A: 149,903,318–149,918,572, reverse strandSV2ASF3B4: 149,923,317–149,928,268, reverse strandSF3B4MTMR11: 149,928,650–149,937,534, reverse strandMTMR11OTUD7B: 149,937,812–150,010,758, reverse strandOTUD7BVPS45: 150,067,279–150,145,329, forward strandVPS45PLEKHO1: 150,149,183–150,164,720, forward strandPLEKHO1ANP32E: 150,217,463–150,236,202, reverse strandANP32ECA14: 150,257,069–150,265,078, forward strandAPH1A: 150,265,042–150,269,580, reverse strandAPH1AC1orf54: 150,268,034–150,281,744, forward strandC1orf54CIART: 150,282,527–150,287,093, forward strandCIARTMRPS21: 150,293,848–150,309,828, forward strandMRPS21PRPF3: 150,321,533–150,353,233, forward strandPRPF3RPRD2: 150,363,091–150,476,999, forward strandRPRD2TARS2: 150,487,325–150,507,614, forward strandTARS2ECM1: 150,507,989–150,515,000, forward strandECM1ADAMTSL4: 150,549,369–150,560,937, forward strandADAMTSL4MCL1: 150,560,895–150,579,738, reverse strandMCL1ENSA: 150,599,671–150,629,633, reverse strandENSAGOLPH3L: 150,638,727–150,697,222, reverse strandGOLPH3LHORMAD1: 150,698,059–150,720,895, reverse strandHORMAD1CTSS: 150,730,079–150,765,957, reverse strandCTSSCTSK: 150,794,880–150,809,577, reverse strandCTSKARNT: 150,808,617–150,876,771, reverse strandARNTDiagram of PRPF3: 16 exons on the forward strand of chromosome 1Exon 10: 1 known disease-causing siteExon 11: 4 known disease-causing sitesExon 1: 150,321,533–150,321,592, 60 basesExon 2: 150,324,895–150,325,087, 193 basesExon 3: 150,325,751–150,325,881, 131 basesExon 4: 150,328,320–150,328,466, 147 basesExon 5: 150,332,684–150,332,767, 84 basesExon 6: 150,332,979–150,333,199, 221 basesExon 7: 150,334,935–150,335,241, 307 basesExon 8: 150,338,160–150,338,326, 167 basesExon 9: 150,340,398–150,340,477, 80 basesExon 10: 150,343,309–150,343,452, 144 basesExon 11: 150,344,162–150,344,261, 100 basesExon 12: 150,344,434–150,344,547, 114 basesExon 13: 150,346,018–150,346,136, 119 basesExon 14: 150,346,408–150,346,491, 84 basesExon 15: 150,349,157–150,349,218, 62 basesExon 16: 150,352,833–150,353,233, 401 bases12468101214165′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 2.4 kb of the gene's 31.7 kb; 2,052 of those bases code for the protein.

    How a genome test reads PRPF3

    6

    positions in PRPF3 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 31.7 kb of PRPF3, introns included, not only the 2.4 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.). PRPF3 gene: pre-mRNA processing factor 3. Retrieved 16 October 2026, from https://dantelabs.com/genes/prpf3

    Vancouver

    Dante Labs. PRPF3 gene: pre-mRNA processing factor 3 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/prpf3

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