Incidental Mutation 'R1456:Specc1l'
ID 161803
Institutional Source Beutler Lab
Gene Symbol Specc1l
Ensembl Gene ENSMUSG00000033444
Gene Name sperm antigen with calponin homology and coiled-coil domains 1-like
Synonyms 9530057A13Rik, Specc1l, 4932439K10Rik, 4930470P14Rik, Cytsa
MMRRC Submission 039511-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.560) question?
Stock # R1456 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 75047872-75148234 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 75082118 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 505 (F505L)
Ref Sequence ENSEMBL: ENSMUSP00000151322 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000040105] [ENSMUST00000105421] [ENSMUST00000218766] [ENSMUST00000219387]
AlphaFold Q2KN98
Predicted Effect possibly damaging
Transcript: ENSMUST00000040105
AA Change: F522L

PolyPhen 2 Score 0.685 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000045099
Gene: ENSMUSG00000033444
AA Change: F522L

DomainStartEndE-ValueType
low complexity region 97 107 N/A INTRINSIC
low complexity region 135 149 N/A INTRINSIC
coiled coil region 255 298 N/A INTRINSIC
low complexity region 376 390 N/A INTRINSIC
coiled coil region 412 467 N/A INTRINSIC
coiled coil region 505 825 N/A INTRINSIC
low complexity region 846 858 N/A INTRINSIC
low complexity region 989 1010 N/A INTRINSIC
CH 1031 1129 1.52e-15 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000105421
AA Change: F522L

PolyPhen 2 Score 0.685 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000101061
Gene: ENSMUSG00000033444
AA Change: F522L

DomainStartEndE-ValueType
low complexity region 80 90 N/A INTRINSIC
low complexity region 118 132 N/A INTRINSIC
coiled coil region 238 281 N/A INTRINSIC
low complexity region 359 373 N/A INTRINSIC
coiled coil region 395 450 N/A INTRINSIC
coiled coil region 488 808 N/A INTRINSIC
low complexity region 829 841 N/A INTRINSIC
low complexity region 972 993 N/A INTRINSIC
CH 1014 1112 1.52e-15 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000218766
AA Change: F505L

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218876
Predicted Effect probably benign
Transcript: ENSMUST00000219387
Meta Mutation Damage Score 0.1435 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.9%
  • 10x: 95.1%
  • 20x: 88.9%
Validation Efficiency 98% (90/92)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a coiled-coil domain containing protein. The encoded protein may play a critical role in actin-cytoskeletal reorganization during facial morphogenesis. Mutations in this gene are a cause of oblique facial clefting-1. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. A read-through transcript composed of SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1-like) and the downstream ADORA2A (adenosine A2a receptor) gene sequence has been identified, but it is thought to be non-coding. [provided by RefSeq, Jun 2013]
PHENOTYPE: Homozygous knockout affects cranial neural crest cell migration, which causes neural tube closure defects and leads to embryonic lethality. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 88 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921504E06Rik C T 2: 19,485,731 (GRCm39) probably null Het
4932414N04Rik A T 2: 68,546,558 (GRCm39) E80V possibly damaging Het
Alkbh3 A G 2: 93,831,764 (GRCm39) probably null Het
Ankar A T 1: 72,704,277 (GRCm39) Y664N probably benign Het
Arhgap18 T C 10: 26,792,436 (GRCm39) I629T probably benign Het
Arhgef28 C T 13: 98,211,510 (GRCm39) E158K probably benign Het
Asxl2 C T 12: 3,551,872 (GRCm39) H1205Y possibly damaging Het
Birc6 A G 17: 74,916,285 (GRCm39) I427V probably benign Het
Camk4 A G 18: 33,262,896 (GRCm39) probably benign Het
Ccdc178 A T 18: 22,283,481 (GRCm39) D16E possibly damaging Het
Cct6b G T 11: 82,644,446 (GRCm39) probably benign Het
Ccz1 A G 5: 143,947,836 (GRCm39) probably benign Het
Cdh23 T C 10: 60,322,899 (GRCm39) N335S possibly damaging Het
Cemip T A 7: 83,647,718 (GRCm39) S121C possibly damaging Het
Cers1 A G 8: 70,783,838 (GRCm39) E262G probably damaging Het
Clec11a G T 7: 43,955,874 (GRCm39) P58T possibly damaging Het
Clec16a T C 16: 10,509,419 (GRCm39) I797T probably damaging Het
Col4a1 A C 8: 11,292,829 (GRCm39) probably benign Het
Colgalt2 G A 1: 152,360,655 (GRCm39) V231I probably damaging Het
D430041D05Rik G T 2: 104,038,428 (GRCm39) N1580K probably damaging Het
Dcdc5 A G 2: 106,181,910 (GRCm39) noncoding transcript Het
Ddx17 T C 15: 79,414,577 (GRCm39) D530G probably benign Het
Dhx9 A T 1: 153,341,441 (GRCm39) D601E probably benign Het
Dnah3 A G 7: 119,646,853 (GRCm39) Y1059H probably damaging Het
Dtx1 C A 5: 120,848,569 (GRCm39) probably benign Het
Egfr A G 11: 16,813,065 (GRCm39) S182G probably benign Het
Fads1 A G 19: 10,163,116 (GRCm39) N131S probably benign Het
Fam243 T A 16: 92,117,553 (GRCm39) Y245F probably damaging Het
Fancm C T 12: 65,165,125 (GRCm39) A1490V possibly damaging Het
Fsd2 C A 7: 81,209,339 (GRCm39) E168* probably null Het
Galnt2l T C 8: 123,568,687 (GRCm39) probably benign Het
Gm9772 A T 17: 22,226,099 (GRCm39) C62S probably damaging Het
H60c C T 10: 3,210,307 (GRCm39) A81T possibly damaging Het
Hira T G 16: 18,744,413 (GRCm39) S377A probably benign Het
Iffo1 T C 6: 125,122,877 (GRCm39) S220P possibly damaging Het
Itih4 A G 14: 30,614,610 (GRCm39) M491V probably benign Het
Khdrbs2 T C 1: 32,559,777 (GRCm39) R102G possibly damaging Het
Klhdc7a T G 4: 139,692,835 (GRCm39) Y704S possibly damaging Het
Klk1b21 G A 7: 43,754,923 (GRCm39) V73I probably benign Het
Krt42 G A 11: 100,160,435 (GRCm39) A88V probably benign Het
Krt42 C T 11: 100,160,436 (GRCm39) A88T probably benign Het
Limk1 G T 5: 134,686,364 (GRCm39) D580E probably benign Het
Lipk C T 19: 34,024,185 (GRCm39) P323S probably damaging Het
Lipo5 T A 19: 33,443,273 (GRCm39) probably benign Het
Llgl2 A G 11: 115,736,325 (GRCm39) D166G probably benign Het
Mapk8ip3 A T 17: 25,125,923 (GRCm39) N439K probably damaging Het
Mapkbp1 C T 2: 119,803,626 (GRCm39) R32W probably damaging Het
Med23 T A 10: 24,779,550 (GRCm39) probably benign Het
Mrgprb1 A T 7: 48,097,777 (GRCm39) M45K probably damaging Het
Mroh7 G A 4: 106,552,338 (GRCm39) probably benign Het
Mrpl27 G A 11: 94,544,659 (GRCm39) probably benign Het
Ms4a10 T A 19: 10,942,097 (GRCm39) T175S possibly damaging Het
Muc17 T C 5: 137,166,799 (GRCm39) H330R probably benign Het
Myo15a A T 11: 60,399,028 (GRCm39) I2787F probably damaging Het
Ndst1 A G 18: 60,846,277 (GRCm39) C11R possibly damaging Het
Obsl1 C A 1: 75,464,300 (GRCm39) G1669* probably null Het
Or5p56 A G 7: 107,589,605 (GRCm39) E11G probably benign Het
Or6c208 A T 10: 129,223,652 (GRCm39) D50V probably damaging Het
Or7e177 T C 9: 20,212,134 (GRCm39) Y214H probably benign Het
Pafah2 T A 4: 134,131,468 (GRCm39) I52N probably damaging Het
Pcsk6 A T 7: 65,693,283 (GRCm39) I693F possibly damaging Het
Pde4c G T 8: 71,199,262 (GRCm39) R228L probably benign Het
Pdzd8 T C 19: 59,288,904 (GRCm39) N832S probably benign Het
Plbd1 T A 6: 136,590,814 (GRCm39) M451L probably benign Het
Pramel14 G T 4: 143,719,851 (GRCm39) D171E probably benign Het
Prom1 T C 5: 44,194,965 (GRCm39) D260G probably damaging Het
Ranbp17 A G 11: 33,216,310 (GRCm39) S813P probably damaging Het
Scn10a T C 9: 119,520,544 (GRCm39) I119V probably benign Het
Sh3pxd2b A G 11: 32,365,967 (GRCm39) T353A probably damaging Het
Shq1 A T 6: 100,646,659 (GRCm39) probably null Het
Slc22a28 T A 19: 8,049,223 (GRCm39) H342L possibly damaging Het
Slco2b1 C T 7: 99,314,114 (GRCm39) E9K probably null Het
Sptan1 G T 2: 29,870,215 (GRCm39) probably null Het
St6gal2 A G 17: 55,797,932 (GRCm39) probably benign Het
Taok2 T C 7: 126,479,313 (GRCm39) I73V probably benign Het
Tax1bp1 C T 6: 52,721,229 (GRCm39) T478I probably benign Het
Tbc1d4 A T 14: 101,744,542 (GRCm39) N361K probably damaging Het
Tph1 A T 7: 46,296,907 (GRCm39) Y429* probably null Het
Tprkb A T 6: 85,901,403 (GRCm39) R14W probably damaging Het
Trio A T 15: 27,753,890 (GRCm39) probably benign Het
Ttc23 T C 7: 67,316,902 (GRCm39) probably benign Het
Vmn1r211 T C 13: 23,036,415 (GRCm39) Y84C probably damaging Het
Vmn2r22 C G 6: 123,614,624 (GRCm39) G322A possibly damaging Het
Wdr74 A G 19: 8,717,776 (GRCm39) Q330R probably benign Het
Wdtc1 C A 4: 133,024,739 (GRCm39) S486I possibly damaging Het
Zbtb24 T C 10: 41,340,989 (GRCm39) V673A possibly damaging Het
Zfpm2 A T 15: 40,965,877 (GRCm39) R655S probably damaging Het
Zkscan5 A G 5: 145,157,798 (GRCm39) N694D probably benign Het
Other mutations in Specc1l
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00549:Specc1l APN 10 75,082,055 (GRCm39) missense probably benign 0.12
IGL01638:Specc1l APN 10 75,082,039 (GRCm39) nonsense probably null
IGL01970:Specc1l APN 10 75,081,595 (GRCm39) missense probably damaging 1.00
IGL02539:Specc1l APN 10 75,103,342 (GRCm39) missense probably benign 0.39
IGL02737:Specc1l APN 10 75,082,158 (GRCm39) missense probably damaging 0.99
IGL02941:Specc1l APN 10 75,077,022 (GRCm39) missense probably benign 0.10
R0305:Specc1l UTSW 10 75,081,663 (GRCm39) missense probably damaging 1.00
R0374:Specc1l UTSW 10 75,084,293 (GRCm39) missense probably damaging 0.99
R0402:Specc1l UTSW 10 75,082,260 (GRCm39) missense probably damaging 1.00
R1508:Specc1l UTSW 10 75,143,072 (GRCm39) missense probably benign 0.00
R1861:Specc1l UTSW 10 75,145,693 (GRCm39) missense probably damaging 1.00
R1869:Specc1l UTSW 10 75,097,659 (GRCm39) missense probably damaging 1.00
R1929:Specc1l UTSW 10 75,081,438 (GRCm39) missense probably damaging 1.00
R1930:Specc1l UTSW 10 75,145,658 (GRCm39) missense probably damaging 1.00
R2021:Specc1l UTSW 10 75,103,425 (GRCm39) critical splice donor site probably null
R2209:Specc1l UTSW 10 75,082,410 (GRCm39) missense probably damaging 1.00
R2271:Specc1l UTSW 10 75,081,438 (GRCm39) missense probably damaging 1.00
R2937:Specc1l UTSW 10 75,094,965 (GRCm39) missense probably damaging 0.98
R4415:Specc1l UTSW 10 75,082,162 (GRCm39) missense possibly damaging 0.92
R4758:Specc1l UTSW 10 75,082,182 (GRCm39) missense probably damaging 0.99
R5344:Specc1l UTSW 10 75,082,007 (GRCm39) missense possibly damaging 0.84
R5383:Specc1l UTSW 10 75,082,539 (GRCm39) missense possibly damaging 0.86
R5426:Specc1l UTSW 10 75,103,384 (GRCm39) missense probably benign 0.21
R5774:Specc1l UTSW 10 75,081,234 (GRCm39) missense probably damaging 1.00
R5788:Specc1l UTSW 10 75,112,755 (GRCm39) missense probably damaging 1.00
R6101:Specc1l UTSW 10 75,084,466 (GRCm39) missense probably damaging 1.00
R6105:Specc1l UTSW 10 75,084,466 (GRCm39) missense probably damaging 1.00
R6136:Specc1l UTSW 10 75,082,494 (GRCm39) missense probably benign 0.38
R6345:Specc1l UTSW 10 75,084,322 (GRCm39) missense probably damaging 0.99
R6459:Specc1l UTSW 10 75,082,001 (GRCm39) missense probably damaging 1.00
R6641:Specc1l UTSW 10 75,082,383 (GRCm39) missense probably damaging 1.00
R6996:Specc1l UTSW 10 75,082,113 (GRCm39) missense probably benign 0.23
R7100:Specc1l UTSW 10 75,081,329 (GRCm39) missense probably benign 0.21
R7475:Specc1l UTSW 10 75,082,281 (GRCm39) missense possibly damaging 0.59
R7545:Specc1l UTSW 10 75,080,921 (GRCm39) missense probably benign 0.00
R7615:Specc1l UTSW 10 75,099,120 (GRCm39) missense probably benign 0.02
R7635:Specc1l UTSW 10 75,112,638 (GRCm39) missense probably damaging 1.00
R7640:Specc1l UTSW 10 75,093,703 (GRCm39) missense probably damaging 1.00
R7682:Specc1l UTSW 10 75,081,636 (GRCm39) missense probably damaging 0.99
R7711:Specc1l UTSW 10 75,066,642 (GRCm39) missense probably benign 0.02
R7742:Specc1l UTSW 10 75,082,251 (GRCm39) missense probably benign 0.01
R7847:Specc1l UTSW 10 75,145,670 (GRCm39) missense probably damaging 0.99
R8015:Specc1l UTSW 10 75,076,902 (GRCm39) missense probably benign 0.17
R8030:Specc1l UTSW 10 75,084,389 (GRCm39) missense probably damaging 1.00
R8882:Specc1l UTSW 10 75,065,689 (GRCm39) start codon destroyed unknown
R9069:Specc1l UTSW 10 75,066,640 (GRCm39) missense probably benign 0.03
R9790:Specc1l UTSW 10 75,066,603 (GRCm39) missense probably benign 0.21
R9791:Specc1l UTSW 10 75,066,603 (GRCm39) missense probably benign 0.21
X0021:Specc1l UTSW 10 75,109,874 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- GCTTGCCTGACAGAACGGATTCAC -3'
(R):5'- GGCCACAGTAGCTTTGTACTCCTC -3'

Sequencing Primer
(F):5'- GGCTGATCTCCAGCAGATTAC -3'
(R):5'- AGTAGCTTTGTACTCCTCCAATGTG -3'
Posted On 2014-03-14