Mutagenetix > Incidental Mutation

Incidental Mutation 'R1929:Specc1l'

215190

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

039947-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.553) question?

Stock #

R1929 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

75047872-75148234 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 75081438 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Phenylalanine at position 278 (S278F)

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: S295F

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000045099
Gene: ENSMUSG00000033444
AA Change: S295F

Domain	Start	End	E-Value	Type
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: S295F

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000101061
Gene: ENSMUSG00000033444
AA Change: S295F

Domain	Start	End	E-Value	Type
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: S278F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000218876

Predicted Effect

probably benign
Transcript: ENSMUST00000219387

Meta Mutation Damage Score

0.4350

Coding Region Coverage

1x: 97.5%
3x: 96.9%
10x: 95.3%
20x: 92.4%

Validation Efficiency

98% (107/109)

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: 103 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adcy10	A	T	1: 165,337,866 (GRCm39)	E160V	probably damaging	Het
Amdhd2	T	C	17: 24,376,860 (GRCm39)		probably null	Het
Angel1	A	C	12: 86,749,093 (GRCm39)	L656V	probably damaging	Het
Ankrd12	G	A	17: 66,293,681 (GRCm39)	S584L	possibly damaging	Het
Apbb2	T	A	5: 66,464,958 (GRCm39)	N679Y	probably benign	Het
Arid3c	T	A	4: 41,724,744 (GRCm39)	I364F	probably damaging	Het
Bcan	T	A	3: 87,900,401 (GRCm39)	S611C	probably damaging	Het
Bnip3	T	G	7: 138,496,359 (GRCm39)		silent	Het
Btc	T	C	5: 91,510,260 (GRCm39)	Y111C	probably damaging	Het
Carnmt1	T	C	19: 18,680,734 (GRCm39)	L336P	probably damaging	Het
Ccdc83	C	T	7: 89,873,285 (GRCm39)	V357I	probably damaging	Het
Cd2bp2	T	C	7: 126,793,050 (GRCm39)	D324G	probably benign	Het
Cdc20b	A	G	13: 113,208,451 (GRCm39)	T216A	probably benign	Het
Cdk17	T	C	10: 93,064,540 (GRCm39)	Y270H	probably damaging	Het
Cenpv	T	C	11: 62,416,059 (GRCm39)	E230G	probably benign	Het
Chst11	T	C	10: 83,027,004 (GRCm39)	Y144H	probably damaging	Het
Cracr2a	T	A	6: 127,584,261 (GRCm39)	F107I	probably damaging	Het
Cyfip1	G	T	7: 55,549,705 (GRCm39)	R624L	probably null	Het
Cyp27b1	T	A	10: 126,884,181 (GRCm39)	V11D	probably damaging	Het
Ddc	T	C	11: 11,785,764 (GRCm39)	N308D	probably damaging	Het
Des	T	G	1: 75,340,137 (GRCm39)	M348R	probably damaging	Het
Dis3l	T	A	9: 64,238,165 (GRCm39)	D109V	probably damaging	Het
Dnah3	T	A	7: 119,574,352 (GRCm39)	I2136F	probably benign	Het
Dnah9	T	C	11: 65,867,224 (GRCm39)	S2785G	probably benign	Het
Dop1a	T	G	9: 86,376,471 (GRCm39)	V235G	probably damaging	Het
Dtx3l	A	T	16: 35,754,059 (GRCm39)	D182E	possibly damaging	Het
Efcab6	A	G	15: 83,777,163 (GRCm39)		probably benign	Het
Elac2	T	A	11: 64,870,015 (GRCm39)	S27T	probably benign	Het
Emsy	T	G	7: 98,275,830 (GRCm39)	K352N	probably damaging	Het
Erbb4	T	C	1: 68,238,047 (GRCm39)	N814S	probably damaging	Het
Fgd6	T	C	10: 93,880,868 (GRCm39)	V574A	probably benign	Het
Filip1	T	C	9: 79,727,212 (GRCm39)	E469G	probably damaging	Het
Fmo1	A	T	1: 162,661,424 (GRCm39)	D286E	probably damaging	Het
Fmo4	A	T	1: 162,626,616 (GRCm39)	I310N	possibly damaging	Het
Focad	A	G	4: 88,260,449 (GRCm39)	N902D	unknown	Het
Focad	A	G	4: 88,315,416 (GRCm39)	S1525G	probably benign	Het
Fras1	T	C	5: 96,815,296 (GRCm39)	W1338R	probably benign	Het
Fry	A	G	5: 150,324,389 (GRCm39)	I1151V	probably null	Het
Garin5b	T	A	7: 4,761,186 (GRCm39)	T509S	probably benign	Het
Gm10076	T	G	14: 105,919,304 (GRCm39)		noncoding transcript	Het
Gm5698	T	G	1: 31,017,042 (GRCm39)	D3A	probably damaging	Het
Gngt2	C	T	11: 95,735,972 (GRCm39)		probably benign	Het
Gsdma	T	C	11: 98,562,193 (GRCm39)		probably null	Het
Gtf2h3	A	T	5: 124,740,262 (GRCm39)		probably benign	Het
Hkdc1	T	C	10: 62,253,677 (GRCm39)	T35A	probably benign	Het
Irs1	T	C	1: 82,266,180 (GRCm39)	S679G	probably benign	Het
Itpr1	T	A	6: 108,470,716 (GRCm39)	C2214S	probably damaging	Het
Kcnh8	GAGACCAACGAGCAGCTGATGCTTCAGA	GAGA	17: 53,032,934 (GRCm39)	74	probably benign	Het
Kcnk16	A	G	14: 20,315,347 (GRCm39)	V72A	probably damaging	Het
Lipa	T	A	19: 34,488,290 (GRCm39)	R119*	probably null	Het
Matr3	T	A	18: 35,721,378 (GRCm39)		probably benign	Het
Med13l	T	G	5: 118,866,898 (GRCm39)	F651V	probably benign	Het
Mfsd11	T	C	11: 116,764,740 (GRCm39)	V388A	probably benign	Het
Mki67	C	T	7: 135,299,794 (GRCm39)	V1747I	possibly damaging	Het
Mms22l	T	C	4: 24,535,936 (GRCm39)		probably benign	Het
Msh5	A	G	17: 35,263,366 (GRCm39)	I154T	probably benign	Het
Myo5b	G	T	18: 74,866,996 (GRCm39)	L1382F	probably damaging	Het
Ncbp2	T	C	16: 31,775,769 (GRCm39)	Y138H	probably damaging	Het
Ndufv1	C	A	19: 4,058,347 (GRCm39)	R359L	probably benign	Het
Ntrk3	A	C	7: 78,166,471 (GRCm39)		probably null	Het
Or1e1c	T	A	11: 73,266,427 (GRCm39)	V287E	probably damaging	Het
Or4a15	A	G	2: 89,193,353 (GRCm39)	V140A	probably benign	Het
Or8b12i	T	A	9: 20,082,705 (GRCm39)	H54L	possibly damaging	Het
P4ha1	A	G	10: 59,206,859 (GRCm39)	E523G	probably damaging	Het
Per3	T	A	4: 151,103,342 (GRCm39)	Y530F	probably damaging	Het
Pes1	C	A	11: 3,919,524 (GRCm39)	L66I	probably damaging	Het
Pigr	G	A	1: 130,774,399 (GRCm39)		probably benign	Het
Pkd1l1	A	T	11: 8,786,197 (GRCm39)		probably benign	Het
Plch1	T	A	3: 63,651,956 (GRCm39)	K378N	probably damaging	Het
Plxnb1	T	C	9: 108,931,776 (GRCm39)		probably null	Het
Pramel22	G	A	4: 143,380,712 (GRCm39)	T437I	probably damaging	Het
Prkdc	A	G	16: 15,472,681 (GRCm39)		probably null	Het
Prrc1	G	T	18: 57,514,718 (GRCm39)	D312Y	probably damaging	Het
Psma5-ps	A	G	10: 85,149,595 (GRCm39)		noncoding transcript	Het
Rab3gap2	T	A	1: 185,015,739 (GRCm39)		probably null	Het
Rgs3	A	G	4: 62,620,384 (GRCm39)	I537V	probably damaging	Het
Rhobtb2	T	G	14: 70,033,893 (GRCm39)	D444A	probably damaging	Het
Rnf40	T	C	7: 127,190,956 (GRCm39)	S314P	probably damaging	Het
Rngtt	T	A	4: 33,500,302 (GRCm39)	C565*	probably null	Het
Samd3	A	G	10: 26,139,884 (GRCm39)		probably benign	Het
Sec61a2	A	G	2: 5,878,547 (GRCm39)		probably benign	Het
Serpina3m	G	A	12: 104,355,581 (GRCm39)	A83T	probably damaging	Het
Serpinb13	A	T	1: 106,926,756 (GRCm39)	I251L	possibly damaging	Het
Sez6	C	T	11: 77,863,758 (GRCm39)	T439I	probably damaging	Het
Shc1	G	A	3: 89,330,849 (GRCm39)	G91S	probably damaging	Het
Slc26a2	A	G	18: 61,331,650 (GRCm39)	C594R	possibly damaging	Het
Spg11	C	T	2: 121,890,688 (GRCm39)	V2044M	probably damaging	Het
Stx18	T	A	5: 38,285,383 (GRCm39)		probably null	Het
Suclg2	T	C	6: 95,566,075 (GRCm39)		probably benign	Het
Tlr4	A	T	4: 66,757,681 (GRCm39)	H158L	probably damaging	Het
Tmem131	A	G	1: 36,851,352 (GRCm39)	V966A	possibly damaging	Het
Tram1l1	T	A	3: 124,115,635 (GRCm39)	I265N	probably damaging	Het
Trim58	T	A	11: 58,531,493 (GRCm39)	F67Y	possibly damaging	Het
Ttc19	A	G	11: 62,172,650 (GRCm39)	Q74R	probably benign	Het
Usp7	T	C	16: 8,516,333 (GRCm39)	S649G	probably benign	Het
Vmn2r16	A	G	5: 109,487,124 (GRCm39)	Y115C	possibly damaging	Het
Zfp444	T	C	7: 6,192,554 (GRCm39)	C191R	probably damaging	Het
Zfp451	A	G	1: 33,821,274 (GRCm39)	F151L	probably damaging	Het
Zfp451	G	A	1: 33,822,937 (GRCm39)	P99S	probably benign	Het
Zfp729b	A	T	13: 67,740,352 (GRCm39)	C648S	probably damaging	Het
Zfp799	A	G	17: 33,040,777 (GRCm39)	Y58H	probably damaging	Het
Zfp804b	A	G	5: 6,819,748 (GRCm39)	V1069A	probably benign	Het
Zfp938	C	T	10: 82,061,381 (GRCm39)	G413D	probably damaging	Het

Other mutations in Specc1l

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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'- GGCATTAGTGAGGACCATTGTG -3'
(R):5'- TCCAGGTTGTCCATGGAGTTAC -3'

Sequencing Primer
(F):5'- CATTAGTGAGGACCATTGTGAAGGTG -3'
(R):5'- ACTGTGCTGATGGTCCATGAG -3'

Posted On

2014-07-14