Mutagenetix > Incidental Mutation

Incidental Mutation 'R1869:Specc1l'

210565

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

039891-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.560) question?

Stock #

R1869 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

75047872-75148234 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 75097659 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 811 (Y811H)

Ref Sequence

ENSEMBL: ENSMUSP00000151322 (fasta)

Gene Model

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

AlphaFold

Q2KN98

Predicted Effect

probably damaging
Transcript: ENSMUST00000040105
AA Change: Y828H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000045099
Gene: ENSMUSG00000033444
AA Change: Y828H

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: Y828H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000101061
Gene: ENSMUSG00000033444
AA Change: Y828H

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: Y811H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000219430

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.4%
20x: 92.9%

Validation Efficiency

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: 127 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921536K21Rik	A	G	11: 3,840,067 (GRCm39)	L110P	probably damaging	Het
6030458C11Rik	T	C	15: 12,817,993 (GRCm39)	D168G	probably damaging	Het
Abca13	A	T	11: 9,242,134 (GRCm39)	E1332D	probably benign	Het
Abhd11	A	G	5: 135,040,471 (GRCm39)	Y168C	probably damaging	Het
Actr5	A	C	2: 158,480,643 (GRCm39)	T554P	probably damaging	Het
Adam34l	A	T	8: 44,078,132 (GRCm39)	Y697*	probably null	Het
Adamts16	A	G	13: 70,883,866 (GRCm39)	L1103P	probably damaging	Het
Adgrb3	A	T	1: 25,865,519 (GRCm39)	I108K	possibly damaging	Het
Agbl4	T	A	4: 111,423,826 (GRCm39)	M284K	possibly damaging	Het
Aoc3	T	A	11: 101,222,293 (GRCm39)	Y176*	probably null	Het
Aox1	A	G	1: 58,115,262 (GRCm39)	E749G	probably damaging	Het
Ap4b1	T	A	3: 103,728,184 (GRCm39)	Y399*	probably null	Het
Arhgef5	A	T	6: 43,265,616 (GRCm39)	I1553F	probably damaging	Het
Bag6	T	C	17: 35,361,802 (GRCm39)	V541A	probably benign	Het
Bdp1	A	C	13: 100,178,709 (GRCm39)	V1879G	probably damaging	Het
Bod1l	G	A	5: 41,991,018 (GRCm39)	S179F	possibly damaging	Het
Bsnd	C	T	4: 106,343,833 (GRCm39)	V158I	probably benign	Het
Cachd1	C	A	4: 100,840,587 (GRCm39)	H880N	probably damaging	Het
Ccdc27	T	C	4: 154,111,220 (GRCm39)		probably null	Het
Cd74	C	T	18: 60,943,484 (GRCm39)	P190S	probably benign	Het
Cep68	A	T	11: 20,190,217 (GRCm39)	L265Q	probably damaging	Het
Cfap70	G	A	14: 20,458,678 (GRCm39)	Q772*	probably null	Het
CK137956	T	A	4: 127,864,327 (GRCm39)	S101C	possibly damaging	Het
Clca3a2	G	A	3: 144,512,164 (GRCm39)	T524M	probably benign	Het
Cxcr6	T	C	9: 123,639,022 (GRCm39)	S15P	probably benign	Het
Cyfip2	T	A	11: 46,114,995 (GRCm39)	Y904F	probably benign	Het
D130040H23Rik	T	A	8: 69,755,354 (GRCm39)	I253N	probably benign	Het
Ddx56	C	T	11: 6,213,993 (GRCm39)	V389M	possibly damaging	Het
Dmp1	A	T	5: 104,359,942 (GRCm39)	D206V	probably damaging	Het
Dnah17	A	T	11: 117,938,015 (GRCm39)	C3350*	probably null	Het
Dst	A	T	1: 34,291,913 (GRCm39)	S877C	probably damaging	Het
Ermp1	A	G	19: 29,623,415 (GRCm39)	S192P	possibly damaging	Het
F13b	G	A	1: 139,438,672 (GRCm39)	D359N	probably benign	Het
Fam171a1	A	T	2: 3,227,189 (GRCm39)	Q769L	possibly damaging	Het
Fap	T	C	2: 62,359,071 (GRCm39)	R411G	probably damaging	Het
Fbn1	A	G	2: 125,193,947 (GRCm39)	V1340A	probably benign	Het
Fbxw19	T	C	9: 109,311,100 (GRCm39)	I370V	probably benign	Het
Foxi1	A	T	11: 34,157,937 (GRCm39)	N29K	possibly damaging	Het
Frem2	T	G	3: 53,442,617 (GRCm39)	D2640A	probably benign	Het
Fzd4	T	C	7: 89,056,454 (GRCm39)	V167A	probably benign	Het
Galnt3	T	C	2: 65,928,123 (GRCm39)	I258V	possibly damaging	Het
Galr2	T	C	11: 116,174,069 (GRCm39)	V233A	possibly damaging	Het
Gldc	G	T	19: 30,116,732 (GRCm39)	Q407K	probably benign	Het
Gmcl1	T	C	6: 86,674,498 (GRCm39)	D460G	probably benign	Het
Gpr89	A	G	3: 96,782,975 (GRCm39)	I325T	probably benign	Het
Grap	T	A	11: 61,555,015 (GRCm39)	Y61N	possibly damaging	Het
Hbs1l	G	T	10: 21,234,305 (GRCm39)		probably null	Het
Hexb	T	A	13: 97,327,767 (GRCm39)	E134D	probably benign	Het
Hydin	T	A	8: 111,227,337 (GRCm39)	V1507D	possibly damaging	Het
Igkv8-16	C	A	6: 70,363,971 (GRCm39)	G17V	probably benign	Het
Kdm4a	T	A	4: 117,996,068 (GRCm39)	Q987L	probably null	Het
Krt76	A	G	15: 101,797,922 (GRCm39)		probably null	Het
Lap3	T	C	5: 45,660,729 (GRCm39)	S238P	probably benign	Het
Letm2	T	C	8: 26,071,729 (GRCm39)	D391G	probably damaging	Het
Lipn	A	G	19: 34,058,139 (GRCm39)	T287A	possibly damaging	Het
Macf1	T	C	4: 123,244,921 (GRCm39)	S466G	probably damaging	Het
Map3k5	C	A	10: 20,007,855 (GRCm39)	S1220*	probably null	Het
Map4	T	A	9: 109,897,996 (GRCm39)	S754R	possibly damaging	Het
Map4	T	C	9: 109,864,032 (GRCm39)	V419A	probably benign	Het
Mroh9	A	G	1: 162,854,082 (GRCm39)	S773P	probably damaging	Het
Mtus1	A	C	8: 41,529,267 (GRCm39)		probably null	Het
Muc1	C	T	3: 89,139,117 (GRCm39)	P533S	probably damaging	Het
Muc13	A	T	16: 33,624,970 (GRCm39)	I282F	probably damaging	Het
Mucl3	A	G	17: 35,949,305 (GRCm39)	L98P	possibly damaging	Het
Myh14	T	A	7: 44,261,067 (GRCm39)	Q1816L	possibly damaging	Het
Nalcn	A	C	14: 123,831,965 (GRCm39)	V103G	possibly damaging	Het
Nlrp9c	G	A	7: 26,084,245 (GRCm39)	Q445*	probably null	Het
Olfml2b	A	G	1: 170,496,812 (GRCm39)	D481G	probably damaging	Het
Or13g1	T	A	7: 85,955,875 (GRCm39)	I149F	possibly damaging	Het
Or2ag19	T	G	7: 106,444,301 (GRCm39)	I161S	probably benign	Het
Or5g23	A	G	2: 85,438,844 (GRCm39)	S137P	probably benign	Het
Or8b37	T	A	9: 37,959,498 (GRCm39)		probably null	Het
Or8k3b	T	A	2: 86,520,735 (GRCm39)	I195F	probably damaging	Het
Pcdhb2	A	T	18: 37,430,408 (GRCm39)		probably null	Het
Pcdhb22	A	C	18: 37,652,200 (GRCm39)	T223P	probably damaging	Het
Pcdhga1	T	A	18: 37,973,143 (GRCm39)	N907K	probably damaging	Het
Pcnt	T	C	10: 76,215,740 (GRCm39)	E2347G	probably null	Het
Phax	T	A	18: 56,706,176 (GRCm39)	V22D	probably benign	Het
Pik3ca	T	C	3: 32,504,499 (GRCm39)	F667S	probably damaging	Het
Pkd1	T	C	17: 24,813,905 (GRCm39)	F4123S	probably damaging	Het
Pkhd1	A	G	1: 20,685,491 (GRCm39)		probably null	Het
Plcb1	G	A	2: 135,152,934 (GRCm39)	R368K	probably benign	Het
Prrc2a	G	T	17: 35,372,284 (GRCm39)	R1739S	possibly damaging	Het
Psg23	A	T	7: 18,348,543 (GRCm39)	M88K	probably benign	Het
Pstk	T	A	7: 130,989,526 (GRCm39)	Y354N	probably damaging	Het
Rab39	A	G	9: 53,617,231 (GRCm39)	I62T	possibly damaging	Het
Ranbp2	A	G	10: 58,328,383 (GRCm39)	I2800V	probably damaging	Het
Rasgrp1	T	C	2: 117,120,828 (GRCm39)	Y431C	probably damaging	Het
Rest	T	A	5: 77,416,209 (GRCm39)	V141E	possibly damaging	Het
Rnf167	T	A	11: 70,540,965 (GRCm39)	I197N	possibly damaging	Het
Rtn1	A	G	12: 72,354,942 (GRCm39)	S335P	probably damaging	Het
Ryr2	G	T	13: 11,676,961 (GRCm39)	R3297S	probably damaging	Het
S1pr3	A	C	13: 51,573,952 (GRCm39)	K378Q	probably benign	Het
Scgb1b24	T	C	7: 33,443,469 (GRCm39)	Y43H	probably damaging	Het
Sh3rf3	T	A	10: 58,919,335 (GRCm39)	M484K	probably damaging	Het
Shank1	A	T	7: 43,991,539 (GRCm39)	R69*	probably null	Het
Siglecf	A	G	7: 43,004,967 (GRCm39)	N399S	probably benign	Het
Slc1a7	A	G	4: 107,865,561 (GRCm39)	T350A	probably damaging	Het
Slc25a54	T	A	3: 108,987,932 (GRCm39)	Y24*	probably null	Het
Slk	T	C	19: 47,613,891 (GRCm39)	F916L	probably damaging	Het
Snap91	T	A	9: 86,672,194 (GRCm39)		probably null	Het
Snrpb2	A	T	2: 142,907,106 (GRCm39)	R25S	possibly damaging	Het
Sprr2h	A	G	3: 92,293,925 (GRCm39)		probably benign	Het
Sult2a5	A	T	7: 13,358,045 (GRCm39)	I26F	probably benign	Het
Syt13	C	T	2: 92,776,448 (GRCm39)	T245I	possibly damaging	Het
Tecrl	T	A	5: 83,502,706 (GRCm39)	T33S	probably benign	Het
Telo2	T	A	17: 25,333,968 (GRCm39)	D93V	probably benign	Het
Tet2	A	T	3: 133,187,202 (GRCm39)		probably null	Het
Tgm7	A	T	2: 120,931,570 (GRCm39)	C198S	probably damaging	Het
Ticrr	T	C	7: 79,328,883 (GRCm39)	F674S	probably damaging	Het
Tmem129	C	A	5: 33,811,843 (GRCm39)	C31F	probably damaging	Het
Tmem132a	T	A	19: 10,836,052 (GRCm39)	D826V	possibly damaging	Het
Tpd52	T	C	3: 9,018,862 (GRCm39)		probably null	Het
Trub2	A	G	2: 29,667,678 (GRCm39)	S321P	probably benign	Het
Ttc29	A	G	8: 79,009,014 (GRCm39)	T295A	probably benign	Het
Tubb1	G	A	2: 174,298,482 (GRCm39)	S89N	probably benign	Het
Tut4	T	A	4: 108,386,497 (GRCm39)	F1122L	probably damaging	Het
Ubap2	C	A	4: 41,233,617 (GRCm39)	G91V	probably damaging	Het
Ugt2b35	A	G	5: 87,149,147 (GRCm39)	N133D	probably damaging	Het
Usp34	A	G	11: 23,314,479 (GRCm39)	H807R	probably benign	Het
Vmn1r220	A	C	13: 23,368,457 (GRCm39)	C80G	probably damaging	Het
Vmn1r79	A	G	7: 11,910,574 (GRCm39)	E152G	probably benign	Het
Vmn2r28	T	C	7: 5,489,345 (GRCm39)	Y498C	probably benign	Het
Wif1	A	G	10: 120,920,824 (GRCm39)	I215M	probably benign	Het
Wnk1	T	C	6: 119,928,050 (GRCm39)	T1134A	probably damaging	Het
Zfp90	A	G	8: 107,145,755 (GRCm39)	H29R	probably benign	Het
Zfp972	A	G	2: 177,563,480 (GRCm39)		probably null	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
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'- AGGTCAGGCAATTGTGTTCAAC -3'
(R):5'- CGGCGTACGGTGATATAGAATAC -3'

Sequencing Primer
(F):5'- CAGGCAATTGTGTTCAACTGGTAC -3'
(R):5'- CATGTGAGCAGAACCATAAGCCTTG -3'

Posted On

2014-06-30