Mutagenetix > Incidental Mutation

Incidental Mutation 'R5426:Specc1l'

426897

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

042992-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.560) question?

Stock #

R5426 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

75047872-75148234 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 75103384 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 920 (S920P)

Ref Sequence

ENSEMBL: ENSMUSP00000101061 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040105] [ENSMUST00000105421] [ENSMUST00000218766]

AlphaFold

Q2KN98

Predicted Effect

probably benign
Transcript: ENSMUST00000040105
AA Change: S920P

PolyPhen 2 Score 0.209 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000045099
Gene: ENSMUSG00000033444
AA Change: S920P

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 benign
Transcript: ENSMUST00000105421
AA Change: S920P

PolyPhen 2 Score 0.209 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000101061
Gene: ENSMUSG00000033444
AA Change: S920P

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 benign
Transcript: ENSMUST00000218766
AA Change: S903P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000219430

Meta Mutation Damage Score

0.0586

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.6%

Validation Efficiency

97% (85/88)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010315B03Rik	T	A	9: 124,056,633 (GRCm39)	H122L	probably damaging	Het
9330182O14Rik	G	A	15: 40,011,932 (GRCm39)	M90I	unknown	Het
9330182O14Rik	G	A	15: 40,011,933 (GRCm39)	D91N	unknown	Het
Abca13	T	A	11: 9,240,722 (GRCm39)	S862T	probably damaging	Het
Acyp2	C	T	11: 30,456,354 (GRCm39)	E98K	possibly damaging	Het
Adgb	C	A	10: 10,226,004 (GRCm39)	A1405S	probably benign	Het
Adpgk	T	A	9: 59,204,832 (GRCm39)	V86E	probably damaging	Het
Agfg2	G	C	5: 137,666,020 (GRCm39)	P80A	probably damaging	Het
Akap11	G	A	14: 78,736,304 (GRCm39)	Q1829*	probably null	Het
Aldh1l1	G	A	6: 90,536,281 (GRCm39)	R62Q	probably benign	Het
Amd1	G	T	10: 40,166,183 (GRCm39)	D265E	probably damaging	Het
Aox4	A	T	1: 58,259,253 (GRCm39)	Q106L	probably damaging	Het
Arap2	A	T	5: 62,800,159 (GRCm39)	N1289K	probably benign	Het
Arhgef12	T	C	9: 42,897,880 (GRCm39)	S874G	probably damaging	Het
Ccdc166	T	C	15: 75,853,945 (GRCm39)	Q45R	possibly damaging	Het
Cdc45	C	T	16: 18,614,647 (GRCm39)	R205H	probably damaging	Het
Cdk14	A	G	5: 4,938,975 (GRCm39)	S388P	possibly damaging	Het
Chgb	A	T	2: 132,635,453 (GRCm39)	Q465L	possibly damaging	Het
Commd9	T	A	2: 101,729,220 (GRCm39)	W109R	probably damaging	Het
Cspg4b	G	A	13: 113,505,587 (GRCm39)	V2239I	probably benign	Het
Cyp2b9	T	C	7: 25,887,080 (GRCm39)	V163A	probably benign	Het
Dcpp2	T	A	17: 24,118,287 (GRCm39)	H27Q	possibly damaging	Het
Ddn	T	A	15: 98,704,347 (GRCm39)	E315V	possibly damaging	Het
Defb29	C	A	2: 152,380,868 (GRCm39)	C47F	probably damaging	Het
Dnah7b	T	C	1: 46,281,366 (GRCm39)	M2809T	possibly damaging	Het
Dock4	A	T	12: 40,795,744 (GRCm39)	I854F	probably damaging	Het
Dsg4	T	C	18: 20,591,541 (GRCm39)	Y427H	probably damaging	Het
E130114P18Rik	C	T	4: 97,578,907 (GRCm39)	A23T	unknown	Het
Flacc1	T	A	1: 58,706,045 (GRCm39)	K275*	probably null	Het
Gemin5	A	G	11: 58,016,113 (GRCm39)	S1297P	probably benign	Het
Gm10309	A	C	17: 86,806,161 (GRCm39)		probably benign	Het
Gpatch11	T	A	17: 79,148,663 (GRCm39)	S155R	possibly damaging	Het
Grin2b	C	A	6: 135,709,366 (GRCm39)	Q1393H	probably damaging	Het
Heatr5b	C	T	17: 79,081,142 (GRCm39)	C1370Y	probably damaging	Het
Hmcn2	C	T	2: 31,226,556 (GRCm39)	T177I	possibly damaging	Het
Ildr1	A	T	16: 36,529,981 (GRCm39)	I123F	probably damaging	Het
Kalrn	A	T	16: 34,083,023 (GRCm39)	V644D	probably damaging	Het
Kifap3	A	G	1: 163,607,440 (GRCm39)	M1V	probably null	Het
Klhl11	A	G	11: 100,354,942 (GRCm39)	L293P	probably damaging	Het
Klrc3	G	A	6: 129,618,513 (GRCm39)	S98L	probably benign	Het
Lrrc37	A	T	11: 103,511,586 (GRCm39)	H127Q	unknown	Het
Med12l	G	A	3: 59,156,143 (GRCm39)	M1220I	probably damaging	Het
Ms4a7	C	T	19: 11,303,166 (GRCm39)		probably null	Het
Mybpc2	A	G	7: 44,159,253 (GRCm39)	V599A	probably benign	Het
Naalad2	T	C	9: 18,258,815 (GRCm39)	N487D	probably benign	Het
Nat8f7	T	G	6: 85,684,805 (GRCm39)	S12R	probably benign	Het
Nefm	T	A	14: 68,357,515 (GRCm39)		probably benign	Het
Nlrp5	T	C	7: 23,117,626 (GRCm39)	V450A	probably damaging	Het
Nps	G	A	7: 134,870,376 (GRCm39)		probably null	Het
Or13c7d	A	G	4: 43,770,168 (GRCm39)	I281T	probably benign	Het
Or2ag16	C	A	7: 106,351,773 (GRCm39)	S274I	probably benign	Het
Or4a74	T	C	2: 89,440,083 (GRCm39)	Y121C	probably damaging	Het
Or4b13	T	A	2: 90,082,955 (GRCm39)	K126*	probably null	Het
Or5e1	T	C	7: 108,354,924 (GRCm39)	L287P	possibly damaging	Het
Or5h24	G	T	16: 58,918,665 (GRCm39)	P230Q	possibly damaging	Het
Or5p67	T	C	7: 107,922,017 (GRCm39)	N289D	probably damaging	Het
Oxct2a	C	A	4: 123,216,506 (GRCm39)	G292W	possibly damaging	Het
Pramel32	T	A	4: 88,547,647 (GRCm39)		probably benign	Het
Prr27	T	C	5: 87,998,744 (GRCm39)		probably benign	Het
Ptx3	T	C	3: 66,128,143 (GRCm39)	M68T	probably damaging	Het
Rufy1	A	G	11: 50,312,561 (GRCm39)	L131S	probably damaging	Het
Septin7	T	A	9: 25,197,986 (GRCm39)	I100N	possibly damaging	Het
Sgms2	T	C	3: 131,135,446 (GRCm39)	I143V	probably benign	Het
Slc25a34	A	G	4: 141,350,877 (GRCm39)	V44A	probably damaging	Het
Slc28a3	T	A	13: 58,710,968 (GRCm39)	D518V	probably damaging	Het
Slc6a7	C	T	18: 61,136,308 (GRCm39)		probably null	Het
Slco4a1	C	A	2: 180,113,028 (GRCm39)	A420D	possibly damaging	Het
Smap1	T	C	1: 23,888,471 (GRCm39)	T180A	probably benign	Het
Tgtp2	A	G	11: 48,950,083 (GRCm39)	M163T	probably benign	Het
Tiam1	G	T	16: 89,662,280 (GRCm39)	Q613K	possibly damaging	Het
Vsig10l	T	A	7: 43,114,247 (GRCm39)	S190T	probably damaging	Het
Vwa3b	A	G	1: 37,154,752 (GRCm39)	Y512C	probably damaging	Het
Wdfy3	T	A	5: 102,067,312 (GRCm39)	N1207Y	probably damaging	Het
Wdr17	C	T	8: 55,134,434 (GRCm39)	G349R	probably damaging	Het
Wdr70	A	G	15: 7,951,586 (GRCm39)	L417S	possibly damaging	Het
Wdr81	A	C	11: 75,341,722 (GRCm39)	S1182A	possibly damaging	Het
Zfp458	A	T	13: 67,405,256 (GRCm39)	C391*	probably null	Het
Zfp638	A	G	6: 83,953,396 (GRCm39)	E1167G	probably damaging	Het
Zfp763	T	A	17: 33,238,569 (GRCm39)	D192V	probably benign	Het
Zfp853	T	G	5: 143,274,624 (GRCm39)	Q332P	unknown	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
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
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'- TGTTTATACCTTACCACAGCAGAAC -3'
(R):5'- CGAAATAGTGTCTTACAGTGGC -3'

Sequencing Primer
(F):5'- CAGCAGAACAAAGGAATTATTCATTG -3'
(R):5'- AAGTCAGTTCAAGGCCAGTCTGTC -3'

Posted On

2016-09-01