Incidental Mutation 'R2359:Cpsf1'
ID 247089
Institutional Source Beutler Lab
Gene Symbol Cpsf1
Ensembl Gene ENSMUSG00000034022
Gene Name cleavage and polyadenylation specific factor 1
Synonyms
MMRRC Submission 040341-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.970) question?
Stock # R2359 (G1)
Quality Score 225
Status Validated
Chromosome 15
Chromosomal Location 76480003-76491791 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 76481873 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 1080 (V1080A)
Ref Sequence ENSEMBL: ENSMUSP00000071794 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000071898] [ENSMUST00000160784] [ENSMUST00000162503] [ENSMUST00000161612] [ENSMUST00000161732] [ENSMUST00000230157] [ENSMUST00000231042]
AlphaFold Q9EPU4
Predicted Effect probably benign
Transcript: ENSMUST00000071898
AA Change: V1080A

PolyPhen 2 Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000071794
Gene: ENSMUSG00000034022
AA Change: V1080A

DomainStartEndE-ValueType
Pfam:MMS1_N 92 684 7.2e-42 PFAM
low complexity region 902 910 N/A INTRINSIC
Pfam:CPSF_A 1071 1407 4.9e-94 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159005
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159049
Predicted Effect noncoding transcript
Transcript: ENSMUST00000160094
Predicted Effect noncoding transcript
Transcript: ENSMUST00000160410
Predicted Effect probably benign
Transcript: ENSMUST00000160784
SMART Domains Protein: ENSMUSP00000124666
Gene: ENSMUSG00000022550

DomainStartEndE-ValueType
transmembrane domain 50 69 N/A INTRINSIC
Pfam:ABC1 188 304 9.2e-38 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000162139
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161783
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161311
Predicted Effect noncoding transcript
Transcript: ENSMUST00000162254
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229007
Predicted Effect probably benign
Transcript: ENSMUST00000162503
SMART Domains Protein: ENSMUSP00000125055
Gene: ENSMUSG00000022550

DomainStartEndE-ValueType
transmembrane domain 50 69 N/A INTRINSIC
Pfam:ABC1 188 304 2.3e-38 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229015
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229367
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229269
Predicted Effect probably benign
Transcript: ENSMUST00000161612
SMART Domains Protein: ENSMUSP00000124701
Gene: ENSMUSG00000022550

DomainStartEndE-ValueType
transmembrane domain 50 69 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000161732
SMART Domains Protein: ENSMUSP00000125482
Gene: ENSMUSG00000022550

DomainStartEndE-ValueType
transmembrane domain 50 69 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000229287
Predicted Effect probably benign
Transcript: ENSMUST00000230157
AA Change: V1080A

PolyPhen 2 Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000231009
Predicted Effect noncoding transcript
Transcript: ENSMUST00000231191
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229437
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229798
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230822
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229982
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229797
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230557
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229504
Predicted Effect probably benign
Transcript: ENSMUST00000231042
Predicted Effect noncoding transcript
Transcript: ENSMUST00000231037
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230149
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230903
Meta Mutation Damage Score 0.0902 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.3%
Validation Efficiency 95% (41/43)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Cleavage and polyadenylation specificity factor (CPSF) is a multisubunit complex that plays a central role in 3-prime processing of pre-mRNAs. CPSF recognizes the AAUAAA signal in the pre-mRNA and interacts with other proteins to facilitate both RNA cleavage and poly(A) synthesis. CPSF1 is the largest subunit of the CPSF complex (Murthy and Manley, 1995 [PubMed 7590244]).[supplied by OMIM, Mar 2008]
Allele List at MGI
Other mutations in this stock
Total: 43 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam24 A G 8: 41,133,984 (GRCm39) E484G possibly damaging Het
Akr1c20 C T 13: 4,573,276 (GRCm39) G13D probably damaging Het
Alkbh3 T C 2: 93,838,458 (GRCm39) T38A probably benign Het
Anxa9 A C 3: 95,210,062 (GRCm39) L99R probably damaging Het
Arfgef2 A T 2: 166,702,539 (GRCm39) Y826F probably damaging Het
Arid2 G T 15: 96,259,759 (GRCm39) L306F probably damaging Het
Ccdc141 C T 2: 77,000,746 (GRCm39) V29M probably damaging Het
Cd55b A G 1: 130,345,858 (GRCm39) S187P probably damaging Het
Cep63 A C 9: 102,471,763 (GRCm39) L526V possibly damaging Het
Chtf8 G T 8: 107,612,048 (GRCm39) probably null Het
Clca4b T A 3: 144,631,003 (GRCm39) S286C probably damaging Het
Csf2rb2 C T 15: 78,176,976 (GRCm39) V165I probably benign Het
Cyp2c40 A T 19: 39,766,398 (GRCm39) V399E probably damaging Het
Dnmt3a T C 12: 3,951,599 (GRCm39) S659P probably damaging Het
Efcab3 T C 11: 104,630,106 (GRCm39) S967P possibly damaging Het
Efr3b G A 12: 4,030,136 (GRCm39) probably benign Het
Epha8 A G 4: 136,673,343 (GRCm39) I147T probably damaging Het
Fbxo48 G A 11: 16,903,602 (GRCm39) W76* probably null Het
Ggt6 A T 11: 72,328,377 (GRCm39) L254F possibly damaging Het
Gm4204 T A 1: 135,159,927 (GRCm39) noncoding transcript Het
Golph3l A G 3: 95,499,275 (GRCm39) probably null Het
Gtf2h3 A G 5: 124,728,939 (GRCm39) K166R probably damaging Het
Hsp90aa1 A G 12: 110,661,003 (GRCm39) probably null Het
Hyi A G 4: 118,217,538 (GRCm39) R79G probably benign Het
Igbp1b G A 6: 138,634,713 (GRCm39) P244S probably damaging Het
Ipo8 G A 6: 148,717,975 (GRCm39) probably benign Het
Larp4b C A 13: 9,208,199 (GRCm39) T391K probably damaging Het
Lrba T C 3: 86,256,057 (GRCm39) V1133A probably benign Het
Med13 C T 11: 86,181,861 (GRCm39) probably benign Het
Ncapd2 A G 6: 125,156,379 (GRCm39) probably benign Het
Neurl1b T C 17: 26,660,569 (GRCm39) F299L probably benign Het
Nosip G A 7: 44,723,450 (GRCm39) A39T possibly damaging Het
Nsd1 A G 13: 55,361,524 (GRCm39) D164G possibly damaging Het
Ntn1 G A 11: 68,276,438 (GRCm39) T170M probably damaging Het
Polrmt A T 10: 79,572,396 (GRCm39) L1079Q probably damaging Het
Prxl2c A T 13: 64,460,465 (GRCm39) C12S probably benign Het
Rab30 A G 7: 92,485,005 (GRCm39) D129G possibly damaging Het
Rwdd2b C T 16: 87,233,809 (GRCm39) S97N probably benign Het
Slitrk3 T G 3: 72,956,678 (GRCm39) D698A possibly damaging Het
Smarcd2 T C 11: 106,157,990 (GRCm39) M93V probably benign Het
Tmprss4 A G 9: 45,097,130 (GRCm39) V45A probably benign Het
Vmn1r22 A T 6: 57,877,974 (GRCm39) M1K probably null Het
Vps13a A G 19: 16,630,043 (GRCm39) probably benign Het
Other mutations in Cpsf1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00499:Cpsf1 APN 15 76,484,416 (GRCm39) missense probably benign 0.27
IGL01013:Cpsf1 APN 15 76,483,497 (GRCm39) nonsense probably null
IGL01599:Cpsf1 APN 15 76,480,741 (GRCm39) missense probably damaging 1.00
IGL02008:Cpsf1 APN 15 76,487,291 (GRCm39) missense probably damaging 1.00
IGL02291:Cpsf1 APN 15 76,487,021 (GRCm39) missense probably damaging 1.00
IGL02901:Cpsf1 APN 15 76,483,696 (GRCm39) nonsense probably null
IGL02929:Cpsf1 APN 15 76,486,327 (GRCm39) critical splice donor site probably null
IGL03402:Cpsf1 APN 15 76,480,203 (GRCm39) splice site probably null
R0005:Cpsf1 UTSW 15 76,484,880 (GRCm39) critical splice donor site probably null
R0044:Cpsf1 UTSW 15 76,483,753 (GRCm39) missense probably benign
R0044:Cpsf1 UTSW 15 76,483,753 (GRCm39) missense probably benign
R0487:Cpsf1 UTSW 15 76,481,202 (GRCm39) missense probably damaging 1.00
R0510:Cpsf1 UTSW 15 76,487,857 (GRCm39) intron probably benign
R0630:Cpsf1 UTSW 15 76,486,171 (GRCm39) missense probably damaging 1.00
R0780:Cpsf1 UTSW 15 76,484,577 (GRCm39) missense probably benign 0.17
R1617:Cpsf1 UTSW 15 76,486,570 (GRCm39) nonsense probably null
R1717:Cpsf1 UTSW 15 76,486,766 (GRCm39) missense possibly damaging 0.77
R1889:Cpsf1 UTSW 15 76,486,356 (GRCm39) missense probably benign 0.06
R1994:Cpsf1 UTSW 15 76,487,360 (GRCm39) missense probably benign 0.03
R2168:Cpsf1 UTSW 15 76,487,937 (GRCm39) missense possibly damaging 0.69
R2697:Cpsf1 UTSW 15 76,483,529 (GRCm39) missense probably damaging 1.00
R2847:Cpsf1 UTSW 15 76,487,051 (GRCm39) missense probably damaging 1.00
R2848:Cpsf1 UTSW 15 76,487,051 (GRCm39) missense probably damaging 1.00
R3409:Cpsf1 UTSW 15 76,485,981 (GRCm39) nonsense probably null
R3410:Cpsf1 UTSW 15 76,485,981 (GRCm39) nonsense probably null
R3815:Cpsf1 UTSW 15 76,485,349 (GRCm39) missense probably benign 0.22
R4030:Cpsf1 UTSW 15 76,485,979 (GRCm39) missense possibly damaging 0.96
R4491:Cpsf1 UTSW 15 76,481,922 (GRCm39) missense possibly damaging 0.85
R4615:Cpsf1 UTSW 15 76,481,137 (GRCm39) missense possibly damaging 0.88
R5227:Cpsf1 UTSW 15 76,483,148 (GRCm39) missense probably damaging 1.00
R5353:Cpsf1 UTSW 15 76,486,771 (GRCm39) missense probably damaging 1.00
R5548:Cpsf1 UTSW 15 76,481,527 (GRCm39) missense possibly damaging 0.95
R5552:Cpsf1 UTSW 15 76,483,846 (GRCm39) missense probably benign 0.27
R5746:Cpsf1 UTSW 15 76,484,037 (GRCm39) missense probably benign 0.01
R6319:Cpsf1 UTSW 15 76,481,167 (GRCm39) missense probably damaging 1.00
R6360:Cpsf1 UTSW 15 76,481,655 (GRCm39) frame shift probably null
R6572:Cpsf1 UTSW 15 76,481,655 (GRCm39) frame shift probably null
R6574:Cpsf1 UTSW 15 76,481,655 (GRCm39) frame shift probably null
R6576:Cpsf1 UTSW 15 76,481,655 (GRCm39) frame shift probably null
R6577:Cpsf1 UTSW 15 76,481,655 (GRCm39) frame shift probably null
R6588:Cpsf1 UTSW 15 76,481,022 (GRCm39) missense probably damaging 1.00
R6595:Cpsf1 UTSW 15 76,486,710 (GRCm39) missense probably damaging 1.00
R6621:Cpsf1 UTSW 15 76,487,719 (GRCm39) missense probably damaging 1.00
R6880:Cpsf1 UTSW 15 76,486,739 (GRCm39) missense probably benign 0.06
R6954:Cpsf1 UTSW 15 76,483,696 (GRCm39) missense probably damaging 1.00
R7100:Cpsf1 UTSW 15 76,480,314 (GRCm39) missense possibly damaging 0.73
R7255:Cpsf1 UTSW 15 76,481,743 (GRCm39) missense probably damaging 1.00
R7318:Cpsf1 UTSW 15 76,481,475 (GRCm39) nonsense probably null
R7371:Cpsf1 UTSW 15 76,484,775 (GRCm39) missense probably damaging 1.00
R7387:Cpsf1 UTSW 15 76,486,766 (GRCm39) missense possibly damaging 0.77
R7446:Cpsf1 UTSW 15 76,485,950 (GRCm39) missense probably benign
R7612:Cpsf1 UTSW 15 76,481,209 (GRCm39) missense probably benign 0.00
R7739:Cpsf1 UTSW 15 76,484,511 (GRCm39) missense probably benign 0.00
R7878:Cpsf1 UTSW 15 76,484,700 (GRCm39) missense probably damaging 1.00
R8334:Cpsf1 UTSW 15 76,487,787 (GRCm39) missense probably benign 0.26
R8345:Cpsf1 UTSW 15 76,485,690 (GRCm39) missense probably benign
R8382:Cpsf1 UTSW 15 76,485,151 (GRCm39) missense probably benign
R8403:Cpsf1 UTSW 15 76,484,483 (GRCm39) missense probably damaging 0.96
R8968:Cpsf1 UTSW 15 76,486,169 (GRCm39) nonsense probably null
R8972:Cpsf1 UTSW 15 76,481,528 (GRCm39) missense probably damaging 1.00
R9257:Cpsf1 UTSW 15 76,484,992 (GRCm39) missense probably benign
R9627:Cpsf1 UTSW 15 76,484,088 (GRCm39) missense probably damaging 0.97
R9776:Cpsf1 UTSW 15 76,486,779 (GRCm39) missense probably damaging 1.00
X0052:Cpsf1 UTSW 15 76,480,502 (GRCm39) missense probably benign 0.04
Predicted Primers PCR Primer
(F):5'- TTTAGGCCTGACACGGTCTC -3'
(R):5'- TCTATGCTGTGGCCACTAGTACC -3'

Sequencing Primer
(F):5'- GACACGGTCTCCTCACTGC -3'
(R):5'- TTGCACTAGGATCCCACGCATG -3'
Posted On 2014-10-30