Incidental Mutation 'R0127:Hapln1'
ID 21474
Institutional Source Beutler Lab
Gene Symbol Hapln1
Ensembl Gene ENSMUSG00000021613
Gene Name hyaluronan and proteoglycan link protein 1
Synonyms LP-1, cartilage linking protein 1, Crtl1l, link protein, CLP, Crtl1
MMRRC Submission 038412-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0127 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 13
Chromosomal Location 89688654-89759951 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 89755988 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Phenylalanine at position 264 (Y264F)
Ref Sequence ENSEMBL: ENSMUSP00000022108 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000022108]
AlphaFold Q9QUP5
Predicted Effect probably benign
Transcript: ENSMUST00000022108
AA Change: Y264F

PolyPhen 2 Score 0.221 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000022108
Gene: ENSMUSG00000021613
AA Change: Y264F

DomainStartEndE-ValueType
IGv 58 143 3.48e-12 SMART
LINK 159 256 7.26e-61 SMART
LINK 260 353 8.35e-52 SMART
Meta Mutation Damage Score 0.1352 question?
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.1%
  • 10x: 95.7%
  • 20x: 90.9%
Validation Efficiency 99% (85/86)
MGI Phenotype PHENOTYPE: Homozygotes for a targeted null mutation exhibit defects in cartilage development and delayed bone formation with short limbs and craniofacial anomalies. Mutants usually die as neonates due to respiratory failure, but some survive and develop dwarfism. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310061N02Rik T C 16: 88,504,342 (GRCm39) T152A probably benign Het
Abca1 T C 4: 53,067,155 (GRCm39) I1351V probably benign Het
Acap1 A T 11: 69,778,043 (GRCm39) probably benign Het
Als2cl T C 9: 110,720,935 (GRCm39) L521P probably damaging Het
Ankrd50 T C 3: 38,510,384 (GRCm39) D661G probably benign Het
Atp6v1b2 T A 8: 69,556,112 (GRCm39) N262K probably damaging Het
Baz1a T A 12: 54,945,491 (GRCm39) D1288V possibly damaging Het
Bbs1 A T 19: 4,945,057 (GRCm39) D371E probably benign Het
Bphl A G 13: 34,248,029 (GRCm39) probably benign Het
Caskin2 C A 11: 115,691,820 (GRCm39) R988S probably damaging Het
Cbr1 C A 16: 93,406,875 (GRCm39) T197N probably damaging Het
Ccdc88c T C 12: 100,901,999 (GRCm39) E1213G possibly damaging Het
Ccna1 A G 3: 54,957,169 (GRCm39) F83L probably damaging Het
Cep290 T A 10: 100,372,787 (GRCm39) probably benign Het
Cep89 C A 7: 35,127,687 (GRCm39) T543K possibly damaging Het
Cmtm7 T C 9: 114,610,738 (GRCm39) M45V probably benign Het
Col16a1 T A 4: 129,946,650 (GRCm39) V91E probably damaging Het
Csmd3 T C 15: 47,845,326 (GRCm39) N920S probably benign Het
Cyp26b1 A G 6: 84,554,190 (GRCm39) probably benign Het
Dao T A 5: 114,158,024 (GRCm39) H215Q probably damaging Het
Dido1 T C 2: 180,313,617 (GRCm39) D885G probably benign Het
Dlx4 T G 11: 95,032,055 (GRCm39) M240L probably benign Het
Dnah5 C T 15: 28,295,071 (GRCm39) P1351L probably damaging Het
Dnah6 T A 6: 73,015,717 (GRCm39) probably benign Het
Dock5 A T 14: 68,083,491 (GRCm39) D139E probably benign Het
Dynlt5 T C 4: 102,859,649 (GRCm39) probably benign Het
Fam234b T C 6: 135,195,821 (GRCm39) probably benign Het
Fat2 T C 11: 55,180,112 (GRCm39) T1410A probably benign Het
Fsip2 T A 2: 82,815,269 (GRCm39) N3667K probably benign Het
Gm5114 T C 7: 39,057,880 (GRCm39) I580V probably benign Het
Heatr5a A G 12: 51,972,188 (GRCm39) V694A probably benign Het
Hps1 A G 19: 42,759,550 (GRCm39) probably benign Het
Igsf9b G T 9: 27,245,681 (GRCm39) R1216L possibly damaging Het
Il4ra G T 7: 125,168,242 (GRCm39) C87F probably damaging Het
Kmt5b A G 19: 3,836,465 (GRCm39) M1V probably null Het
Krit1 A G 5: 3,872,178 (GRCm39) E401G probably damaging Het
Lamp1 T C 8: 13,224,491 (GRCm39) V385A probably damaging Het
Ly6g5b A G 17: 35,333,567 (GRCm39) Y82H probably damaging Het
Mapre2 A G 18: 23,937,232 (GRCm39) I25V probably benign Het
Mep1a A G 17: 43,808,777 (GRCm39) probably benign Het
Mkrn1 A G 6: 39,376,209 (GRCm39) W466R probably benign Het
Muc2 C A 7: 141,302,691 (GRCm39) F11L probably benign Het
Nebl T A 2: 17,397,794 (GRCm39) M501L probably benign Het
Oga A T 19: 45,760,327 (GRCm39) I277N probably damaging Het
Or11g2 A G 14: 50,855,789 (GRCm39) I37V probably benign Het
Or4p18 A G 2: 88,232,699 (GRCm39) V193A probably benign Het
Or5w8 A G 2: 87,687,827 (GRCm39) I103V probably benign Het
Or8g32 A G 9: 39,305,238 (GRCm39) I50M probably benign Het
Pkd1l2 A G 8: 117,776,787 (GRCm39) probably benign Het
Pkhd1l1 A G 15: 44,418,001 (GRCm39) M2886V probably damaging Het
Pop5 T A 5: 115,378,230 (GRCm39) L58H probably damaging Het
Prkch C A 12: 73,768,561 (GRCm39) H444N possibly damaging Het
Reln T C 5: 22,209,134 (GRCm39) D1148G probably damaging Het
Rffl G A 11: 82,703,458 (GRCm39) T120M probably damaging Het
Rmdn2 A T 17: 79,977,998 (GRCm39) S320C probably damaging Het
Rrbp1 C T 2: 143,831,864 (GRCm39) R101H probably benign Het
Rtf1 G A 2: 119,557,224 (GRCm39) R443H probably damaging Het
Serac1 G T 17: 6,099,115 (GRCm39) L559I probably damaging Het
Slc12a1 A G 2: 125,061,682 (GRCm39) R958G probably damaging Het
Slc15a3 T A 19: 10,833,350 (GRCm39) W456R probably damaging Het
Slc28a2b T A 2: 122,347,550 (GRCm39) probably null Het
Slc35f5 C T 1: 125,503,942 (GRCm39) P290L probably damaging Het
Slc35g2 C T 9: 100,435,170 (GRCm39) R167Q probably benign Het
Spag4 T C 2: 155,909,962 (GRCm39) V302A probably damaging Het
Spire2 A C 8: 124,084,836 (GRCm39) probably benign Het
Sptbn2 G T 19: 4,774,772 (GRCm39) V142L probably damaging Het
Syt17 T A 7: 118,009,164 (GRCm39) D352V probably damaging Het
Tars3 A T 7: 65,314,717 (GRCm39) D425V probably benign Het
Thsd7a A G 6: 12,554,907 (GRCm39) S326P probably benign Het
Tnpo2 T C 8: 85,767,257 (GRCm39) S64P probably damaging Het
Tonsl G T 15: 76,517,685 (GRCm39) A678D probably benign Het
Trim12c A G 7: 103,990,113 (GRCm39) probably null Het
Tsc22d1 A G 14: 76,656,421 (GRCm39) T885A possibly damaging Het
Ttn T C 2: 76,572,542 (GRCm39) D26117G probably damaging Het
Ttn T A 2: 76,707,355 (GRCm39) probably benign Het
Ugt3a1 T C 15: 9,306,342 (GRCm39) F164L probably benign Het
Vmn2r89 A G 14: 51,693,160 (GRCm39) N170S probably damaging Het
Vrk2 G T 11: 26,484,313 (GRCm39) probably benign Het
Wt1 C A 2: 104,963,802 (GRCm39) D207E probably damaging Het
Zbtb46 G A 2: 181,053,608 (GRCm39) A368V probably benign Het
Zc3h13 A T 14: 75,560,694 (GRCm39) D428V unknown Het
Zcchc8 C G 5: 123,845,400 (GRCm39) G320A probably damaging Het
Znfx1 T C 2: 166,886,130 (GRCm39) E810G possibly damaging Het
Other mutations in Hapln1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00235:Hapln1 APN 13 89,756,261 (GRCm39) missense probably benign 0.00
IGL00494:Hapln1 APN 13 89,753,590 (GRCm39) missense probably benign 0.04
IGL01865:Hapln1 APN 13 89,749,784 (GRCm39) missense probably damaging 1.00
IGL02706:Hapln1 APN 13 89,753,578 (GRCm39) missense possibly damaging 0.86
IGL02990:Hapln1 APN 13 89,749,725 (GRCm39) missense probably benign 0.03
R0033:Hapln1 UTSW 13 89,749,932 (GRCm39) missense probably benign 0.20
R0058:Hapln1 UTSW 13 89,755,997 (GRCm39) missense probably benign 0.17
R0058:Hapln1 UTSW 13 89,755,997 (GRCm39) missense probably benign 0.17
R0519:Hapln1 UTSW 13 89,732,835 (GRCm39) start gained probably benign
R3862:Hapln1 UTSW 13 89,753,418 (GRCm39) nonsense probably null
R3982:Hapln1 UTSW 13 89,753,560 (GRCm39) missense probably benign
R4717:Hapln1 UTSW 13 89,753,579 (GRCm39) missense probably benign 0.11
R4861:Hapln1 UTSW 13 89,749,571 (GRCm39) missense possibly damaging 0.65
R4861:Hapln1 UTSW 13 89,749,571 (GRCm39) missense possibly damaging 0.65
R4862:Hapln1 UTSW 13 89,749,571 (GRCm39) missense possibly damaging 0.65
R4899:Hapln1 UTSW 13 89,749,769 (GRCm39) missense possibly damaging 0.90
R5402:Hapln1 UTSW 13 89,753,530 (GRCm39) missense probably benign 0.07
R5629:Hapln1 UTSW 13 89,749,634 (GRCm39) missense probably damaging 0.98
R6019:Hapln1 UTSW 13 89,756,219 (GRCm39) missense probably benign 0.45
R7917:Hapln1 UTSW 13 89,755,997 (GRCm39) missense probably benign 0.17
R7938:Hapln1 UTSW 13 89,753,347 (GRCm39) missense probably damaging 0.99
R8312:Hapln1 UTSW 13 89,749,563 (GRCm39) missense probably benign
R8345:Hapln1 UTSW 13 89,732,902 (GRCm39) missense probably benign
Z1088:Hapln1 UTSW 13 89,749,617 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- TGTGTGAGCACACGCCAAGAAG -3'
(R):5'- TGGGAAACCTACAAAGCGCACTG -3'

Sequencing Primer
(F):5'- CCAAGAAGCAAGGCTAAAGC -3'
(R):5'- AGCCTCAGTCGGACTGC -3'
Posted On 2013-04-11