Incidental Mutation 'R1055:Clrn1'
ID 94252
Institutional Source Beutler Lab
Gene Symbol Clrn1
Ensembl Gene ENSMUSG00000043850
Gene Name clarin 1
Synonyms clarin-1, USH3, Ush3a, A130002D11Rik
MMRRC Submission 039145-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1055 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 58751449-58792633 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 58772531 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 117 (I117F)
Ref Sequence ENSEMBL: ENSMUSP00000052254 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000051408] [ENSMUST00000055636] [ENSMUST00000072551]
AlphaFold Q8K445
Predicted Effect probably benign
Transcript: ENSMUST00000051408
AA Change: I99F

PolyPhen 2 Score 0.089 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000051738
Gene: ENSMUSG00000043850
AA Change: I99F

DomainStartEndE-ValueType
Pfam:Claudin_2 18 208 1.8e-11 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000055636
AA Change: I117F

PolyPhen 2 Score 0.385 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000052254
Gene: ENSMUSG00000043850
AA Change: I117F

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
transmembrane domain 116 138 N/A INTRINSIC
transmembrane domain 153 175 N/A INTRINSIC
transmembrane domain 207 229 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000072551
SMART Domains Protein: ENSMUSP00000072363
Gene: ENSMUSG00000043850

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
SCOP:d1hw7a_ 65 87 5e-3 SMART
transmembrane domain 129 151 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161419
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.3%
  • 10x: 95.3%
  • 20x: 87.5%
Validation Efficiency 100% (58/58)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIIa. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele exhibit progressive hearing loss and loss of balance associated with defects in outer hair cells and supporting cells. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930578I06Rik A G 14: 64,210,724 (GRCm39) V168A possibly damaging Het
A1cf C A 19: 31,909,919 (GRCm39) T237N probably benign Het
Actl10 A T 2: 154,394,588 (GRCm39) Q180L probably benign Het
Adcy1 T C 11: 7,059,075 (GRCm39) L327P probably damaging Het
Adcy7 T C 8: 89,044,685 (GRCm39) probably benign Het
Ahctf1 G A 1: 179,591,051 (GRCm39) T1243I possibly damaging Het
Akap6 C T 12: 52,927,455 (GRCm39) Q122* probably null Het
Apob G A 12: 8,044,963 (GRCm39) G861D probably damaging Het
Arhgef11 A C 3: 87,624,425 (GRCm39) T539P probably benign Het
Cd244a T A 1: 171,404,844 (GRCm39) V232E probably damaging Het
Chia1 A C 3: 106,038,199 (GRCm39) D365A probably damaging Het
Clpsl2 C T 17: 28,768,500 (GRCm39) Q5* probably null Het
Csmd3 A G 15: 47,744,933 (GRCm39) L1354P probably damaging Het
Csn2 G A 5: 87,842,596 (GRCm39) P144S possibly damaging Het
Dcdc2a T A 13: 25,286,593 (GRCm39) M172K probably damaging Het
Dnah9 A T 11: 66,050,837 (GRCm39) W152R probably damaging Het
Dnmt3a T A 12: 3,922,864 (GRCm39) S82T probably benign Het
Ebf1 A G 11: 44,523,602 (GRCm39) K146E probably damaging Het
Gfpt2 A C 11: 49,718,038 (GRCm39) R504S probably damaging Het
Gpank1 T A 17: 35,343,284 (GRCm39) S255T probably damaging Het
Greb1 T C 12: 16,732,252 (GRCm39) M1570V probably damaging Het
Gtf2i A T 5: 134,292,478 (GRCm39) I403K probably damaging Het
Hoxc11 T A 15: 102,863,270 (GRCm39) C104S probably damaging Het
Hsh2d G A 8: 72,954,304 (GRCm39) D229N probably benign Het
Ilrun T C 17: 27,986,910 (GRCm39) N272S probably damaging Het
Khdrbs2 A T 1: 32,683,238 (GRCm39) probably benign Het
Lix1l G T 3: 96,528,626 (GRCm39) G200V probably damaging Het
Lrrc23 T C 6: 124,755,114 (GRCm39) N141S probably damaging Het
Marchf11 A T 15: 26,309,748 (GRCm39) D134V probably damaging Het
Myo9a A T 9: 59,762,653 (GRCm39) T795S probably benign Het
Nhsl1 T A 10: 18,401,223 (GRCm39) D782E probably benign Het
Nptxr T C 15: 79,674,456 (GRCm39) probably benign Het
Nrp1 A G 8: 129,195,079 (GRCm39) M512V possibly damaging Het
Ofcc1 C T 13: 40,362,305 (GRCm39) G206R probably benign Het
Or12e7 ATTGCTACTC A 2: 87,287,781 (GRCm39) probably benign Het
Or5b3 G A 19: 13,388,754 (GRCm39) A274T probably benign Het
Pard3 T C 8: 128,104,761 (GRCm39) F267S probably benign Het
Pomt2 G A 12: 87,194,254 (GRCm39) T50M possibly damaging Het
Qsox2 A G 2: 26,104,137 (GRCm39) Y298H probably damaging Het
Rabgap1 A G 2: 37,382,080 (GRCm39) K450E possibly damaging Het
Rpa1 A T 11: 75,193,558 (GRCm39) V591D probably damaging Het
Sall3 A C 18: 81,013,007 (GRCm39) M1143R probably benign Het
Scgb1b19 G T 7: 32,986,768 (GRCm39) A13S unknown Het
Scn1a T C 2: 66,168,340 (GRCm39) T89A probably benign Het
Sdk2 C T 11: 113,729,472 (GRCm39) silent Het
Sdr42e1 T G 8: 118,390,323 (GRCm39) N106T probably damaging Het
Shpk A T 11: 73,105,945 (GRCm39) M266L probably benign Het
Slc34a1 G T 13: 55,550,846 (GRCm39) R139L probably benign Het
Smbd1 C A 16: 32,627,088 (GRCm39) D67Y probably damaging Het
Srd5a3 A G 5: 76,301,485 (GRCm39) N238S probably benign Het
Tmprss2 T C 16: 97,377,462 (GRCm39) N212D probably damaging Het
Uap1 G T 1: 169,984,480 (GRCm39) probably benign Het
Ugt1a6a A G 1: 88,066,736 (GRCm39) M181V probably benign Het
Vmn2r32 C T 7: 7,477,326 (GRCm39) W355* probably null Het
Vmn2r86 T A 10: 130,282,226 (GRCm39) S797C probably damaging Het
Wiz A G 17: 32,606,616 (GRCm39) S40P probably damaging Het
Zfand6 A G 7: 84,265,181 (GRCm39) probably benign Het
Zfp280d G A 9: 72,236,449 (GRCm39) probably null Het
Other mutations in Clrn1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01065:Clrn1 APN 3 58,792,446 (GRCm39) missense probably damaging 0.99
IGL03184:Clrn1 APN 3 58,753,645 (GRCm39) missense probably benign 0.00
IGL03187:Clrn1 APN 3 58,753,854 (GRCm39) missense probably damaging 0.99
R0015:Clrn1 UTSW 3 58,753,848 (GRCm39) missense probably damaging 0.99
R0015:Clrn1 UTSW 3 58,753,848 (GRCm39) missense probably damaging 0.99
R2301:Clrn1 UTSW 3 58,753,773 (GRCm39) missense probably damaging 1.00
R4753:Clrn1 UTSW 3 58,792,318 (GRCm39) missense probably damaging 1.00
R5493:Clrn1 UTSW 3 58,753,837 (GRCm39) missense probably damaging 1.00
R5916:Clrn1 UTSW 3 58,753,783 (GRCm39) missense probably benign 0.13
R6393:Clrn1 UTSW 3 58,753,741 (GRCm39) missense probably damaging 1.00
R6719:Clrn1 UTSW 3 58,753,861 (GRCm39) missense probably damaging 0.99
R7722:Clrn1 UTSW 3 58,753,755 (GRCm39) missense possibly damaging 0.52
R8824:Clrn1 UTSW 3 58,792,314 (GRCm39) missense probably benign 0.12
R9342:Clrn1 UTSW 3 58,792,251 (GRCm39) missense probably benign 0.01
R9681:Clrn1 UTSW 3 58,792,251 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- AGGACATCCTTTCACAGACTGAAAAGC -3'
(R):5'- ATCTTTGGGCAAAACCCCTGGC -3'

Sequencing Primer
(F):5'- TCACAGACTGAAAAGCACTTTGTC -3'
(R):5'- CCCCTGGCAAATTGGTAAGTG -3'
Posted On 2014-01-05