Incidental Mutation 'R7475:Specc1l'
ID 579433
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 045549-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.560) question?
Stock # R7475 (G1)
Quality Score 225.009
Status Validated
Chromosome 10
Chromosomal Location 75047872-75148234 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 75082281 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 559 (L559Q)
Ref Sequence ENSEMBL: ENSMUSP00000151322 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000040105] [ENSMUST00000105421] [ENSMUST00000218766] [ENSMUST00000219387]
AlphaFold Q2KN98
Predicted Effect probably damaging
Transcript: ENSMUST00000040105
AA Change: L576Q

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000045099
Gene: ENSMUSG00000033444
AA Change: L576Q

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 probably damaging
Transcript: ENSMUST00000105421
AA Change: L576Q

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000101061
Gene: ENSMUSG00000033444
AA Change: L576Q

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 possibly damaging
Transcript: ENSMUST00000218766
AA Change: L559Q

PolyPhen 2 Score 0.592 (Sensitivity: 0.87; Specificity: 0.91)
Predicted Effect probably benign
Transcript: ENSMUST00000219387
Meta Mutation Damage Score 0.1795 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency 99% (77/78)
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: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc5 G T 16: 20,218,739 (GRCm39) N214K probably benign Het
Abcf1 A G 17: 36,274,459 (GRCm39) probably null Het
Agxt2 A T 15: 10,409,623 (GRCm39) M508L probably benign Het
Akr1c21 A T 13: 4,626,318 (GRCm39) Y114F probably benign Het
Amz1 T C 5: 140,729,941 (GRCm39) probably null Het
Ank1 G T 8: 23,622,646 (GRCm39) A1732S probably benign Het
Atg16l1 T C 1: 87,687,805 (GRCm39) S50P possibly damaging Het
AW551984 A G 9: 39,509,236 (GRCm39) S302P probably damaging Het
Ccn6 T A 10: 39,034,296 (GRCm39) Y102F probably damaging Het
Ces3a T A 8: 105,780,322 (GRCm39) probably null Het
Dedd C A 1: 171,167,881 (GRCm39) P185Q probably benign Het
Fam186a A T 15: 99,845,395 (GRCm39) V283E unknown Het
Fat2 C A 11: 55,194,479 (GRCm39) V1187F probably benign Het
Fbxw11 T C 11: 32,661,999 (GRCm39) probably null Het
Fcgbp C T 7: 27,802,401 (GRCm39) T1443I probably damaging Het
Foxj2 A G 6: 122,814,801 (GRCm39) D279G probably benign Het
Gbp5 A G 3: 142,207,122 (GRCm39) D97G probably damaging Het
Gm49368 A T 7: 127,707,154 (GRCm39) T661S possibly damaging Het
Gria4 T G 9: 4,513,330 (GRCm39) T260P probably damaging Het
Gtf2ird2 T A 5: 134,230,267 (GRCm39) D195E possibly damaging Het
Hectd4 T A 5: 121,496,196 (GRCm39) probably null Het
Ifngr2 G A 16: 91,354,797 (GRCm39) C32Y unknown Het
Ikzf5 A T 7: 130,993,788 (GRCm39) C280S probably benign Het
Ints9 G T 14: 65,263,914 (GRCm39) E395D probably null Het
Isoc2b T C 7: 4,854,084 (GRCm39) D96G probably benign Het
Jmjd1c T G 10: 67,061,092 (GRCm39) S967R probably benign Het
Kcnj3 A T 2: 55,327,338 (GRCm39) K42N probably benign Het
Kiz T C 2: 146,733,006 (GRCm39) V394A possibly damaging Het
Knl1 A T 2: 118,918,027 (GRCm39) H1795L probably damaging Het
Lmntd2 A G 7: 140,790,602 (GRCm39) probably null Het
Loxhd1 C A 18: 77,500,001 (GRCm39) D1690E possibly damaging Het
Lrp1b T C 2: 41,234,588 (GRCm39) D1121G Het
Map3k2 T C 18: 32,333,015 (GRCm39) V63A possibly damaging Het
Mcc G T 18: 44,609,303 (GRCm39) A499D probably damaging Het
Mcpt9 T A 14: 56,264,400 (GRCm39) I232F probably damaging Het
Meltf A G 16: 31,700,756 (GRCm39) K92R probably benign Het
Mff T A 1: 82,723,159 (GRCm39) probably null Het
Mrgpra3 T A 7: 47,239,695 (GRCm39) Y77F probably damaging Het
Mylk G A 16: 34,734,446 (GRCm39) probably null Het
Ndufv2 A G 17: 66,394,532 (GRCm39) V111A possibly damaging Het
Nkd2 T C 13: 73,973,861 (GRCm39) E99G probably damaging Het
Nlk C A 11: 78,474,225 (GRCm39) G358V probably damaging Het
Nnmt A T 9: 48,503,532 (GRCm39) C165S probably damaging Het
Nxpe4 T A 9: 48,304,640 (GRCm39) C242* probably null Het
Oas1b A T 5: 120,955,705 (GRCm39) N162I probably damaging Het
Or4s2 A G 2: 88,473,554 (GRCm39) I148V probably benign Het
Otog A G 7: 45,916,700 (GRCm39) N879S probably damaging Het
Pcsk7 T A 9: 45,838,923 (GRCm39) Y612N probably damaging Het
Peg10 CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG CCACATCAGGATCCACATCAGGATGCACATCAG 6: 4,756,398 (GRCm39) probably benign Het
Pgbd5 T C 8: 125,160,750 (GRCm39) D39G probably benign Het
Pkhd1l1 C T 15: 44,368,581 (GRCm39) Q800* probably null Het
Pkn3 T C 2: 29,977,122 (GRCm39) S621P probably benign Het
Polr3c T C 3: 96,622,501 (GRCm39) I385V probably benign Het
Ppp1r21 G T 17: 88,863,031 (GRCm39) G257W probably benign Het
Prkn A G 17: 11,653,501 (GRCm39) D199G probably benign Het
Pxylp1 C T 9: 96,738,420 (GRCm39) probably null Het
Rasgrp1 T C 2: 117,116,589 (GRCm39) T613A probably benign Het
Robo3 C T 9: 37,336,674 (GRCm39) V387I probably benign Het
Rxfp2 T A 5: 149,973,046 (GRCm39) Y174N possibly damaging Het
Sec24a T C 11: 51,604,379 (GRCm39) M746V probably damaging Het
Sema4f T A 6: 82,891,355 (GRCm39) E571D possibly damaging Het
Septin3 T C 15: 82,170,657 (GRCm39) V217A probably benign Het
Serpinb1b A C 13: 33,277,548 (GRCm39) K260N probably benign Het
Sin3b A G 8: 73,476,500 (GRCm39) T645A possibly damaging Het
Sobp C T 10: 42,897,830 (GRCm39) R585Q probably damaging Het
Srxn1 C T 2: 151,947,573 (GRCm39) probably benign Het
Sspo G A 6: 48,432,794 (GRCm39) R890Q probably benign Het
Stard9 A G 2: 120,518,591 (GRCm39) D505G probably damaging Het
Tjp1 A T 7: 64,972,087 (GRCm39) I653K probably damaging Het
Tnks C T 8: 35,298,866 (GRCm39) E1296K probably damaging Het
Ttbk2 A T 2: 120,579,121 (GRCm39) I667N probably benign Het
Usp24 T C 4: 106,199,550 (GRCm39) S165P possibly damaging Het
Usp46 T A 5: 74,189,598 (GRCm39) K109* probably null Het
Vmn1r191 A G 13: 22,362,942 (GRCm39) C271R probably benign Het
Zfp592 T C 7: 80,673,200 (GRCm39) S55P probably damaging Het
Zmynd15 T C 11: 70,351,867 (GRCm39) S158P probably benign Het
Zscan22 T G 7: 12,640,664 (GRCm39) C303G probably damaging 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
R1456:Specc1l UTSW 10 75,082,118 (GRCm39) missense probably damaging 0.98
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
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'- GAATGCCCGTTTTGAGCGAG -3'
(R):5'- GGGTATGAGCCAGATCTTCC -3'

Sequencing Primer
(F):5'- AGAGCAGCTTCTAGGTGTGCAG -3'
(R):5'- GTATGAGCCAGATCTTCCTGCAG -3'
Posted On 2019-10-07