Incidental Mutation 'IGL03184:Clrn1'
ID 412371
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Clrn1
Ensembl Gene ENSMUSG00000043850
Gene Name clarin 1
Synonyms clarin-1, USH3, Ush3a, A130002D11Rik
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # IGL03184
Quality Score
Status
Chromosome 3
Chromosomal Location 58751449-58792633 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 58753645 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Serine at position 239 (T239S)
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: T221S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000051738
Gene: ENSMUSG00000043850
AA Change: T221S

DomainStartEndE-ValueType
Pfam:Claudin_2 18 208 1.8e-11 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000055636
AA Change: T239S

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000052254
Gene: ENSMUSG00000043850
AA Change: T239S

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
AA Change: T161S

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000072363
Gene: ENSMUSG00000043850
AA Change: T161S

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
Coding Region Coverage
Validation Efficiency
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: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2210408I21Rik T C 13: 77,471,570 (GRCm39) Y992H possibly damaging Het
Actmap A G 7: 26,896,432 (GRCm39) probably benign Het
Adcy7 T A 8: 89,035,271 (GRCm39) D58E probably benign Het
Aff2 G A X: 68,810,840 (GRCm39) V404M possibly damaging Het
Ankhd1 T A 18: 36,780,830 (GRCm39) L1961M probably damaging Het
Brms1l T C 12: 55,915,062 (GRCm39) *324Q probably null Het
Bub1b T C 2: 118,440,258 (GRCm39) probably benign Het
Cacna1b A G 2: 24,548,501 (GRCm39) probably null Het
Clta T C 4: 44,025,514 (GRCm39) Y145H probably benign Het
Coro6 T C 11: 77,354,779 (GRCm39) V14A probably damaging Het
Cyp4a30b A G 4: 115,316,216 (GRCm39) D314G probably damaging Het
Fn1 T C 1: 71,648,656 (GRCm39) N1418D probably benign Het
Fshr A C 17: 89,354,068 (GRCm39) L97V possibly damaging Het
Gcm2 T C 13: 41,258,888 (GRCm39) Q152R probably damaging Het
Gcnt2 A G 13: 41,041,660 (GRCm39) N273S probably benign Het
Gm11437 A T 11: 84,047,090 (GRCm39) probably benign Het
Gm4559 A G 7: 141,828,046 (GRCm39) S19P unknown Het
Igsf8 T G 1: 172,146,199 (GRCm39) I462R probably damaging Het
Kirrel3 T C 9: 34,919,052 (GRCm39) F243S probably damaging Het
Krt80 C T 15: 101,250,135 (GRCm39) V37M probably damaging Het
Lama4 T C 10: 38,954,839 (GRCm39) Y1131H probably damaging Het
Mrpl21 T C 19: 3,342,529 (GRCm39) probably benign Het
Mtcl1 T C 17: 66,661,209 (GRCm39) N923S probably benign Het
Nectin2 G A 7: 19,472,231 (GRCm39) P53S possibly damaging Het
Nup98 G A 7: 101,832,752 (GRCm39) T335I probably damaging Het
Or2y1e C A 11: 49,218,568 (GRCm39) T110K probably damaging Het
Or4a74 T C 2: 89,439,912 (GRCm39) D178G probably damaging Het
Or4e5 A G 14: 52,728,380 (GRCm39) S14P probably benign Het
Or51a42 T A 7: 103,708,054 (GRCm39) I252F probably damaging Het
Or6c69c T C 10: 129,910,627 (GRCm39) M116T possibly damaging Het
Pcdhb14 A G 18: 37,582,085 (GRCm39) E397G probably benign Het
Pcgf5 T G 19: 36,412,076 (GRCm39) probably benign Het
Pclo C T 5: 14,764,457 (GRCm39) P1025L probably damaging Het
Pdcd1lg2 C A 19: 29,431,911 (GRCm39) F226L probably benign Het
Pik3ca T A 3: 32,494,035 (GRCm39) S332R probably benign Het
Plek A T 11: 16,931,887 (GRCm39) D321E probably benign Het
Pm20d2 A G 4: 33,179,241 (GRCm39) F333L probably damaging Het
Polk T C 13: 96,620,491 (GRCm39) T570A probably benign Het
Rpgrip1l G A 8: 92,027,437 (GRCm39) L201F probably damaging Het
Serpinb2 T A 1: 107,452,607 (GRCm39) L395H probably damaging Het
Slc9c1 T G 16: 45,368,003 (GRCm39) S197R probably damaging Het
Smg1 T A 7: 117,779,603 (GRCm39) E1264V possibly damaging Het
Sned1 A G 1: 93,202,390 (GRCm39) D678G probably benign Het
Sorcs2 A G 5: 36,188,556 (GRCm39) S851P probably benign Het
Srcap A G 7: 127,129,674 (GRCm39) probably benign Het
Tbck T C 3: 132,441,864 (GRCm39) Y557H probably damaging Het
Tfap2d T C 1: 19,189,110 (GRCm39) S219P probably damaging Het
Trim9 T C 12: 70,297,995 (GRCm39) D570G probably damaging Het
Usp25 A G 16: 76,878,541 (GRCm39) Y655C probably damaging Het
Utrn T A 10: 12,585,910 (GRCm39) T956S probably benign Het
Vmn1r68 T A 7: 10,261,799 (GRCm39) I100F probably benign Het
Vps13a A T 19: 16,631,734 (GRCm39) S2634T probably benign Het
Zfp472 T A 17: 33,196,390 (GRCm39) L155* probably null Het
Zfp808 A G 13: 62,317,381 (GRCm39) I43M possibly damaging Het
Other mutations in Clrn1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01065:Clrn1 APN 3 58,792,446 (GRCm39) missense probably damaging 0.99
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
R1055:Clrn1 UTSW 3 58,772,531 (GRCm39) missense probably benign 0.38
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
Posted On 2016-08-02