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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O95602: Variant p.Cys1562Phe

DNA-directed RNA polymerase I subunit RPA1
Gene: POLR1A
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Variant information Variant position: help 1562 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help LP/P [Disclaimer] The variants are classified into three categories: LP/P, LB/B and US.
  • LP/P: likely pathogenic or pathogenic.
  • LB/B: likely benign or benign.
  • US: uncertain significance
Residue change: help From Cysteine (C) to Phenylalanine (F) at position 1562 (C1562F, p.Cys1562Phe). Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.
Physico-chemical properties: help Change from medium size and polar (C) to large size and aromatic (F) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -2 The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:
  • Lowest score: -4 (low probability of substitution).
  • Highest score: 11 (high probability of substitution).
More information can be found on the following page
Variant description: help In AFDCIN; pathogenic; results in increased rRNA transcription in transfected cells. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 1562 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1720 The length of the canonical sequence.
Location on the sequence: help SLVVSLAHGAVIYATKGITR C LLNETTNNKNEKELVLNTEG The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.
Residue conservation: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         SLVVSLAHGAVIYATKGITRCLLNETTNNKNEKELVLNTEG

Mouse                         SLVVSLAHKAIVYTTKGITRCLLNETTNSKNEKELVLNTEG

Rat                           SLVVSLAHNAIVYTTKGITRCLLNETINSKNEKEFVLNTEG

Drosophila                    SIIRELAGKSVVHQVQHIKRAIIYKG----NDDDQLLKTDG

Slime mold                    GIVETEASKFVLKSCKGITRCFVNEK-QVGGKTHYSIQSEG

Baker's yeast                 NIVEEICRKSIIRQIPHIDRCVHPEP----ENGKRVLVTEG

Fission yeast                 SLVEKACSETVIHEIPGITRCFSKPP-DSALDTVPKVITEG
Sequence annotation in neighborhood: help The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:
  • Type: the type of sequence feature.
  • Positions: endpoints of the sequence feature.
  • Description: contains additional information about the feature.
TypePositionsDescription
Chain 1 – 1720 DNA-directed RNA polymerase I subunit RPA1
Beta strand 1559 – 1566



Literature citations
POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies.
Smallwood K.; Watt K.E.N.; Ide S.; Baltrunaite K.; Brunswick C.; Inskeep K.; Capannari C.; Adam M.P.; Begtrup A.; Bertola D.R.; Demmer L.; Demo E.; Devinsky O.; Gallagher E.R.; Guillen Sacoto M.J.; Jech R.; Keren B.; Kussmann J.; Ladda R.; Lansdon L.A.; Lunke S.; Mardy A.; McWalters K.; Person R.; Raiti L.; Saitoh N.; Saunders C.J.; Schnur R.; Skorvanek M.; Sell S.L.; Slavotinek A.; Sullivan B.R.; Stark Z.; Symonds J.D.; Wenger T.; Weber S.; Whalen S.; White S.M.; Winkelmann J.; Zech M.; Zeidler S.; Maeshima K.; Stottmann R.W.; Trainor P.A.; Weaver K.N.;
Am. J. Hum. Genet. 110:809-825(2023)
Cited for: VARIANTS AFDCIN VAL-59; HIS-393; LYS-481; ILE-496; ILE-1241; 1284-GLN--ARG-1720 DEL; GLU-1330 DEL; PHE-1562; MET-1631 AND LEU-1638; INVOLVEMENT IN AFDCIN; CHARACTERIZATION OF VARIANTS AFDCIN VAL-59; HIS-393; GLN-593; GLU-1330 DEL AND PHE-1562;
Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.