Incidental Mutation 'R3545:Clip1'
ID 268160
Institutional Source Beutler Lab
Gene Symbol Clip1
Ensembl Gene ENSMUSG00000049550
Gene Name CAP-GLY domain containing linker protein 1
Synonyms Rsn, CLIP-170, 4631429H07Rik, restin, Clip 170, 1110007I12Rik, Clip50, cytoplasmic linker protein 50
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R3545 (G1)
Quality Score 225
Status Not validated
Chromosome 5
Chromosomal Location 123715857-123822527 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 123769141 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 532 (L532P)
Ref Sequence ENSEMBL: ENSMUSP00000031382 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031382] [ENSMUST00000063905] [ENSMUST00000111561] [ENSMUST00000111564] [ENSMUST00000111566] [ENSMUST00000149410]
AlphaFold Q922J3
Predicted Effect probably damaging
Transcript: ENSMUST00000031382
AA Change: L532P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000031382
Gene: ENSMUSG00000049550
AA Change: L532P

DomainStartEndE-ValueType
internal_repeat_2 11 53 2.28e-5 PROSPERO
CAP_GLY 60 125 1.05e-31 SMART
internal_repeat_2 140 177 2.28e-5 PROSPERO
CAP_GLY 213 278 4.69e-34 SMART
low complexity region 286 304 N/A INTRINSIC
low complexity region 305 331 N/A INTRINSIC
coiled coil region 349 451 N/A INTRINSIC
coiled coil region 474 535 N/A INTRINSIC
coiled coil region 581 620 N/A INTRINSIC
coiled coil region 652 1352 N/A INTRINSIC
low complexity region 1362 1373 N/A INTRINSIC
Pfam:CLIP1_ZNF 1375 1392 5.8e-9 PFAM
ZnF_C2HC 1417 1433 1.45e0 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000063905
AA Change: L521P

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000068241
Gene: ENSMUSG00000049550
AA Change: L521P

DomainStartEndE-ValueType
internal_repeat_2 11 53 3.3e-5 PROSPERO
CAP_GLY 60 125 1.05e-31 SMART
internal_repeat_2 140 177 3.3e-5 PROSPERO
CAP_GLY 213 278 4.69e-34 SMART
low complexity region 286 304 N/A INTRINSIC
low complexity region 305 331 N/A INTRINSIC
coiled coil region 349 524 N/A INTRINSIC
coiled coil region 570 609 N/A INTRINSIC
coiled coil region 641 1075 N/A INTRINSIC
coiled coil region 1115 1235 N/A INTRINSIC
low complexity region 1245 1256 N/A INTRINSIC
ZnF_C2HC 1300 1316 1.45e0 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000111561
AA Change: L521P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000107186
Gene: ENSMUSG00000049550
AA Change: L521P

DomainStartEndE-ValueType
internal_repeat_2 11 53 1.93e-5 PROSPERO
CAP_GLY 60 125 1.05e-31 SMART
internal_repeat_2 140 177 1.93e-5 PROSPERO
CAP_GLY 213 278 4.69e-34 SMART
low complexity region 286 304 N/A INTRINSIC
low complexity region 305 331 N/A INTRINSIC
coiled coil region 349 524 N/A INTRINSIC
coiled coil region 570 609 N/A INTRINSIC
coiled coil region 641 1341 N/A INTRINSIC
low complexity region 1351 1362 N/A INTRINSIC
ZnF_C2HC 1406 1422 1.45e0 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000111564
AA Change: L486P

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000107190
Gene: ENSMUSG00000049550
AA Change: L486P

DomainStartEndE-ValueType
internal_repeat_2 11 53 2.5e-5 PROSPERO
CAP_GLY 60 125 1.05e-31 SMART
internal_repeat_2 140 177 2.5e-5 PROSPERO
CAP_GLY 213 278 4.69e-34 SMART
low complexity region 286 304 N/A INTRINSIC
low complexity region 305 331 N/A INTRINSIC
coiled coil region 349 489 N/A INTRINSIC
coiled coil region 535 574 N/A INTRINSIC
coiled coil region 606 1230 N/A INTRINSIC
low complexity region 1240 1251 N/A INTRINSIC
ZnF_C2HC 1295 1311 1.45e0 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000111566
AA Change: L486P

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000107192
Gene: ENSMUSG00000049550
AA Change: L486P

DomainStartEndE-ValueType
internal_repeat_2 11 53 2e-5 PROSPERO
CAP_GLY 60 125 1.05e-31 SMART
internal_repeat_2 140 177 2e-5 PROSPERO
CAP_GLY 213 278 4.69e-34 SMART
low complexity region 286 304 N/A INTRINSIC
low complexity region 305 331 N/A INTRINSIC
coiled coil region 349 489 N/A INTRINSIC
coiled coil region 535 574 N/A INTRINSIC
coiled coil region 606 1306 N/A INTRINSIC
low complexity region 1316 1327 N/A INTRINSIC
ZnF_C2HC 1371 1387 1.45e0 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000122603
Predicted Effect probably benign
Transcript: ENSMUST00000149410
AA Change: L455P

PolyPhen 2 Score 0.044 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000115965
Gene: ENSMUSG00000049550
AA Change: L455P

DomainStartEndE-ValueType
low complexity region 26 32 N/A INTRINSIC
CAP_GLY 60 125 1.05e-31 SMART
CAP_GLY 213 278 4.69e-34 SMART
low complexity region 286 304 N/A INTRINSIC
low complexity region 305 331 N/A INTRINSIC
coiled coil region 334 458 N/A INTRINSIC
coiled coil region 504 543 N/A INTRINSIC
coiled coil region 575 827 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000137363
AA Change: L273P
SMART Domains Protein: ENSMUSP00000121425
Gene: ENSMUSG00000049550
AA Change: L273P

DomainStartEndE-ValueType
CAP_GLY 2 31 2.59e0 SMART
low complexity region 39 57 N/A INTRINSIC
low complexity region 58 84 N/A INTRINSIC
coiled coil region 101 276 N/A INTRINSIC
coiled coil region 322 361 N/A INTRINSIC
coiled coil region 393 980 N/A INTRINSIC
low complexity region 991 1002 N/A INTRINSIC
Pfam:CLIP1_ZNF 1004 1021 4.2e-9 PFAM
ZnF_C2HC 1046 1062 1.45e0 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000199018
Predicted Effect probably benign
Transcript: ENSMUST00000144121
SMART Domains Protein: ENSMUSP00000119641
Gene: ENSMUSG00000049550

DomainStartEndE-ValueType
CAP_GLY 37 102 1.05e-31 SMART
Meta Mutation Damage Score 0.1822 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.7%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene links endocytic vesicles to microtubules. This gene is highly expressed in Reed-Sternberg cells of Hodgkin disease. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
PHENOTYPE: Mice homozygous for a targeted allele display reduced male fertility and teratozoospermia. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 34 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ankrd28 A G 14: 31,437,217 (GRCm39) L646S probably benign Het
Efl1 A T 7: 82,412,018 (GRCm39) E802D probably benign Het
F11r T C 1: 171,288,829 (GRCm39) V149A probably damaging Het
Fhit T C 14: 9,870,095 (GRCm38) T125A probably benign Het
Fmn2 A G 1: 174,330,192 (GRCm39) D194G unknown Het
Gdi1 T A X: 73,351,414 (GRCm39) F175L possibly damaging Het
Herc3 T C 6: 58,833,670 (GRCm39) S186P probably damaging Het
Hexa A G 9: 59,464,581 (GRCm39) N157S probably damaging Het
Kdm1b C T 13: 47,216,553 (GRCm39) R308W probably damaging Het
Lig1 T A 7: 13,026,089 (GRCm39) N281K possibly damaging Het
Lrp1b A T 2: 40,490,300 (GRCm39) L287H probably damaging Het
Mcf2 T C X: 59,180,806 (GRCm39) K74R probably damaging Het
Nat1 A G 8: 67,943,684 (GRCm39) D23G possibly damaging Het
Nbeal1 T C 1: 60,317,939 (GRCm39) F1959L probably damaging Het
Ncf1 T A 5: 134,255,463 (GRCm39) K143* probably null Het
Nid2 T A 14: 19,813,779 (GRCm39) Y195N probably damaging Het
Nlrp9a T C 7: 26,256,757 (GRCm39) I125T probably benign Het
Nme7 T C 1: 164,213,351 (GRCm39) F343S probably damaging Het
Otud4 A G 8: 80,391,684 (GRCm39) E443G probably damaging Het
Palld G T 8: 62,003,112 (GRCm39) A329E possibly damaging Het
Pask A T 1: 93,244,837 (GRCm39) V1095D probably damaging Het
Pdzd2 C T 15: 12,375,557 (GRCm39) R1526Q probably benign Het
Prkcq A G 2: 11,288,627 (GRCm39) K527E probably benign Het
Ramac T A 7: 81,418,270 (GRCm39) probably null Het
Reln A G 5: 22,432,598 (GRCm39) V134A possibly damaging Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Septin9 T C 11: 117,243,499 (GRCm39) I350T probably damaging Het
Slc16a7 T A 10: 125,130,569 (GRCm39) K39* probably null Het
Spata32 T C 11: 103,101,570 (GRCm39) E21G possibly damaging Het
Tbc1d1 G A 5: 64,443,350 (GRCm39) R523Q probably damaging Het
Thnsl1 T G 2: 21,217,438 (GRCm39) D397E probably benign Het
Tubal3 T G 13: 3,983,560 (GRCm39) *447G probably null Het
Uprt T A X: 103,526,934 (GRCm39) L123H probably damaging Het
Usp9x T C X: 12,994,629 (GRCm39) L940P probably benign Het
Other mutations in Clip1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00159:Clip1 APN 5 123,741,717 (GRCm39) missense possibly damaging 0.94
IGL01067:Clip1 APN 5 123,768,867 (GRCm39) missense probably damaging 0.99
IGL01524:Clip1 APN 5 123,717,442 (GRCm39) missense probably damaging 1.00
IGL01632:Clip1 APN 5 123,755,559 (GRCm39) missense probably damaging 1.00
IGL01798:Clip1 APN 5 123,721,612 (GRCm39) missense probably damaging 1.00
IGL01874:Clip1 APN 5 123,741,729 (GRCm39) missense possibly damaging 0.50
IGL01908:Clip1 APN 5 123,761,270 (GRCm39) splice site probably benign
IGL02120:Clip1 APN 5 123,785,946 (GRCm39) missense probably damaging 1.00
IGL02309:Clip1 APN 5 123,755,763 (GRCm39) missense probably damaging 0.99
IGL02555:Clip1 APN 5 123,759,857 (GRCm39) critical splice donor site probably null
IGL03027:Clip1 APN 5 123,759,919 (GRCm39) missense probably benign 0.43
IGL03336:Clip1 APN 5 123,791,633 (GRCm39) nonsense probably null
IGL03365:Clip1 APN 5 123,721,649 (GRCm39) missense probably damaging 1.00
IGL02802:Clip1 UTSW 5 123,769,186 (GRCm39) missense probably damaging 1.00
PIT4812001:Clip1 UTSW 5 123,768,738 (GRCm39) missense probably benign 0.08
R0254:Clip1 UTSW 5 123,755,395 (GRCm39) splice site probably benign
R0401:Clip1 UTSW 5 123,791,852 (GRCm39) missense probably damaging 1.00
R0530:Clip1 UTSW 5 123,778,594 (GRCm39) missense probably damaging 1.00
R0744:Clip1 UTSW 5 123,768,784 (GRCm39) missense probably benign 0.05
R0833:Clip1 UTSW 5 123,768,784 (GRCm39) missense probably benign 0.05
R1116:Clip1 UTSW 5 123,717,554 (GRCm39) missense probably damaging 0.99
R1182:Clip1 UTSW 5 123,785,928 (GRCm39) missense probably damaging 1.00
R1656:Clip1 UTSW 5 123,768,466 (GRCm39) missense possibly damaging 0.61
R1700:Clip1 UTSW 5 123,768,433 (GRCm39) missense probably benign
R1889:Clip1 UTSW 5 123,791,559 (GRCm39) missense probably damaging 0.99
R1975:Clip1 UTSW 5 123,761,281 (GRCm39) missense possibly damaging 0.79
R2406:Clip1 UTSW 5 123,741,723 (GRCm39) missense probably damaging 1.00
R3547:Clip1 UTSW 5 123,769,141 (GRCm39) missense probably damaging 1.00
R3548:Clip1 UTSW 5 123,769,141 (GRCm39) missense probably damaging 1.00
R3911:Clip1 UTSW 5 123,728,897 (GRCm39) missense probably damaging 1.00
R3944:Clip1 UTSW 5 123,755,892 (GRCm39) unclassified probably benign
R4660:Clip1 UTSW 5 123,717,437 (GRCm39) missense probably damaging 0.98
R4784:Clip1 UTSW 5 123,717,356 (GRCm39) missense probably damaging 1.00
R4785:Clip1 UTSW 5 123,717,356 (GRCm39) missense probably damaging 1.00
R4824:Clip1 UTSW 5 123,769,086 (GRCm39) missense probably damaging 1.00
R4831:Clip1 UTSW 5 123,721,664 (GRCm39) missense probably damaging 1.00
R4951:Clip1 UTSW 5 123,768,408 (GRCm39) missense probably benign 0.02
R4960:Clip1 UTSW 5 123,792,066 (GRCm39) nonsense probably null
R5014:Clip1 UTSW 5 123,755,793 (GRCm39) missense probably damaging 0.99
R5116:Clip1 UTSW 5 123,768,770 (GRCm39) missense probably benign 0.05
R5212:Clip1 UTSW 5 123,768,744 (GRCm39) missense probably benign 0.09
R5238:Clip1 UTSW 5 123,785,946 (GRCm39) missense probably damaging 1.00
R5318:Clip1 UTSW 5 123,751,147 (GRCm39) unclassified probably benign
R5372:Clip1 UTSW 5 123,768,303 (GRCm39) missense probably benign 0.02
R5701:Clip1 UTSW 5 123,751,366 (GRCm39) unclassified probably benign
R5734:Clip1 UTSW 5 123,753,217 (GRCm39) unclassified probably benign
R5757:Clip1 UTSW 5 123,765,460 (GRCm39) missense probably benign 0.21
R6024:Clip1 UTSW 5 123,753,152 (GRCm39) missense possibly damaging 0.66
R6160:Clip1 UTSW 5 123,751,604 (GRCm39) missense possibly damaging 0.66
R6177:Clip1 UTSW 5 123,751,897 (GRCm39) unclassified probably benign
R6183:Clip1 UTSW 5 123,780,667 (GRCm39) missense probably damaging 1.00
R6377:Clip1 UTSW 5 123,741,717 (GRCm39) missense possibly damaging 0.50
R6436:Clip1 UTSW 5 123,779,848 (GRCm39) missense probably damaging 1.00
R6471:Clip1 UTSW 5 123,778,612 (GRCm39) missense probably damaging 0.99
R6766:Clip1 UTSW 5 123,752,827 (GRCm39) unclassified probably benign
R7015:Clip1 UTSW 5 123,751,675 (GRCm39) unclassified probably benign
R7094:Clip1 UTSW 5 123,761,333 (GRCm39) missense probably benign 0.02
R7143:Clip1 UTSW 5 123,791,673 (GRCm39) missense probably benign
R7222:Clip1 UTSW 5 123,749,904 (GRCm39) missense probably damaging 0.99
R7233:Clip1 UTSW 5 123,749,922 (GRCm39) missense probably damaging 1.00
R7238:Clip1 UTSW 5 123,751,328 (GRCm39) missense
R7249:Clip1 UTSW 5 123,741,663 (GRCm39) missense probably damaging 1.00
R7283:Clip1 UTSW 5 123,751,857 (GRCm39) missense
R7295:Clip1 UTSW 5 123,765,419 (GRCm39) missense probably benign 0.19
R7447:Clip1 UTSW 5 123,791,696 (GRCm39) missense probably benign 0.03
R7458:Clip1 UTSW 5 123,778,609 (GRCm39) missense probably damaging 1.00
R7483:Clip1 UTSW 5 123,755,447 (GRCm39) missense probably benign 0.00
R7516:Clip1 UTSW 5 123,721,448 (GRCm39) missense probably benign 0.00
R7619:Clip1 UTSW 5 123,752,342 (GRCm39) missense
R7831:Clip1 UTSW 5 123,751,342 (GRCm39) missense
R7897:Clip1 UTSW 5 123,760,861 (GRCm39) missense probably benign
R8155:Clip1 UTSW 5 123,751,699 (GRCm39) missense
R8157:Clip1 UTSW 5 123,768,782 (GRCm39) missense probably benign 0.17
R8232:Clip1 UTSW 5 123,785,981 (GRCm39) missense probably benign 0.05
R8396:Clip1 UTSW 5 123,780,627 (GRCm39) missense probably damaging 1.00
R8446:Clip1 UTSW 5 123,794,008 (GRCm39) missense probably damaging 1.00
R8486:Clip1 UTSW 5 123,752,770 (GRCm39) unclassified probably benign
R8511:Clip1 UTSW 5 123,791,969 (GRCm39) missense possibly damaging 0.50
R8731:Clip1 UTSW 5 123,752,756 (GRCm39) missense
R8889:Clip1 UTSW 5 123,717,565 (GRCm39) missense probably benign 0.00
R8892:Clip1 UTSW 5 123,717,565 (GRCm39) missense probably benign 0.00
R9058:Clip1 UTSW 5 123,752,645 (GRCm39) missense
R9106:Clip1 UTSW 5 123,753,223 (GRCm39) missense probably damaging 0.97
R9212:Clip1 UTSW 5 123,721,399 (GRCm39) missense probably damaging 1.00
R9217:Clip1 UTSW 5 123,717,441 (GRCm39) missense probably damaging 1.00
R9223:Clip1 UTSW 5 123,784,337 (GRCm39) missense probably damaging 1.00
R9325:Clip1 UTSW 5 123,751,186 (GRCm39) missense
R9752:Clip1 UTSW 5 123,760,009 (GRCm39) missense probably damaging 1.00
Z1177:Clip1 UTSW 5 123,755,413 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- GTGTGCAGAGCCTTGATCTC -3'
(R):5'- ATTATCTCCCTGTGCGAGC -3'

Sequencing Primer
(F):5'- AGAGCCTTGATCTCCTTCTGAAACG -3'
(R):5'- ACCCTTACATGTGATAGGCG -3'
Posted On 2015-02-19