Mutagenetix > Incidental Mutation

Incidental Mutation 'R9069:Specc1l'

689438

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

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.560) question?

Stock #

R9069 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

75047872-75148234 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 75066640 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 30 (N30D)

Ref Sequence

ENSEMBL: ENSMUSP00000151322 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040105] [ENSMUST00000105421] [ENSMUST00000218766] [ENSMUST00000219387]

AlphaFold

Q2KN98

Predicted Effect

probably benign
Transcript: ENSMUST00000040105
AA Change: N47D

PolyPhen 2 Score 0.091 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000045099
Gene: ENSMUSG00000033444
AA Change: N47D

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: N47D

PolyPhen 2 Score 0.091 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000101061
Gene: ENSMUSG00000033444
AA Change: N47D

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: N30D

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)

Predicted Effect

probably benign
Transcript: ENSMUST00000219387
AA Change: N30D

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (78/78)

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
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aars2	T	A	17: 45,818,523 (GRCm39)	C103S	probably damaging	Het
Adamts20	T	C	15: 94,236,349 (GRCm39)	S841G	probably benign	Het
Add3	T	A	19: 53,222,332 (GRCm39)	V313E	possibly damaging	Het
Ahr	G	T	12: 35,562,771 (GRCm39)		probably benign	Het
Ankrd12	T	A	17: 66,356,874 (GRCm39)	M48L	probably benign	Het
Apaf1	A	C	10: 90,859,580 (GRCm39)		probably null	Het
Bank1	T	C	3: 135,989,772 (GRCm39)	H106R	probably benign	Het
Birc6	A	G	17: 74,868,260 (GRCm39)		probably benign	Het
Castor1	A	G	11: 4,170,141 (GRCm39)	E73G	probably benign	Het
Ccdc170	C	T	10: 4,511,016 (GRCm39)	H692Y	possibly damaging	Het
Cd93	A	G	2: 148,284,071 (GRCm39)	I425T	probably benign	Het
Celsr1	A	C	15: 85,914,772 (GRCm39)	L1067R	possibly damaging	Het
Clca3a2	A	T	3: 144,519,447 (GRCm39)		probably benign	Het
Col14a1	T	C	15: 55,251,990 (GRCm39)	S549P	unknown	Het
Col6a4	A	G	9: 105,952,138 (GRCm39)	S587P	possibly damaging	Het
Crebbp	C	A	16: 3,903,187 (GRCm39)	M2017I	probably benign	Het
Crybg1	A	C	10: 43,874,103 (GRCm39)	F1002V	probably benign	Het
Ctif	T	C	18: 75,654,458 (GRCm39)	E356G	probably damaging	Het
Dbx2	T	C	15: 95,530,239 (GRCm39)	K243E	probably damaging	Het
Dgkh	C	T	14: 78,853,957 (GRCm39)	V394I	probably damaging	Het
Dnaja4	T	A	9: 54,621,638 (GRCm39)	M321K	probably benign	Het
Dock9	T	C	14: 121,866,324 (GRCm39)	N593S	probably damaging	Het
Dot1l	T	A	10: 80,626,560 (GRCm39)	S1260R	probably damaging	Het
Eea1	A	T	10: 95,831,510 (GRCm39)	L200F	probably damaging	Het
Elp2	T	G	18: 24,765,833 (GRCm39)	F658V	probably benign	Het
Fbxw15	G	A	9: 109,394,468 (GRCm39)	Q116*	probably null	Het
Fstl5	A	T	3: 76,615,416 (GRCm39)	N826Y	probably damaging	Het
Galp	T	C	7: 6,214,347 (GRCm39)	S60P	possibly damaging	Het
Gm7298	G	T	6: 121,761,393 (GRCm39)	M1316I	probably benign	Het
Gsdmc	T	C	15: 63,649,902 (GRCm39)	M330V	probably benign	Het
Hectd2	T	C	19: 36,562,862 (GRCm39)	F175L	probably benign	Het
Hmbs	A	G	9: 44,248,102 (GRCm39)	I318T	possibly damaging	Het
Ifi205	T	C	1: 173,855,841 (GRCm39)	D63G	probably benign	Het
Il10ra	T	A	9: 45,167,396 (GRCm39)	Q387L	probably damaging	Het
Kcnj14	C	A	7: 45,469,388 (GRCm39)	G39V	probably benign	Het
Kpna1	T	C	16: 35,836,381 (GRCm39)		probably benign	Het
Lrp2	A	T	2: 69,331,996 (GRCm39)	D1586E	probably damaging	Het
Lrrc45	A	G	11: 120,607,947 (GRCm39)	I243V	probably benign	Het
Lrrc7	T	C	3: 157,946,138 (GRCm39)	K187R	probably benign	Het
Mamdc4	G	T	2: 25,453,371 (GRCm39)	T1216N	probably damaging	Het
Map1a	A	C	2: 121,134,145 (GRCm39)	K1654Q	probably benign	Het
Mta2	G	A	19: 8,924,104 (GRCm39)	V195M	probably damaging	Het
Nav2	G	T	7: 49,208,561 (GRCm39)	R1583L	probably damaging	Het
Or2y1g	A	T	11: 49,171,247 (GRCm39)	T91S	probably benign	Het
Or4c112	A	T	2: 88,854,308 (GRCm39)	L13Q	probably damaging	Het
Or9i14	T	C	19: 13,792,735 (GRCm39)	Y73C	probably damaging	Het
Osbpl1a	T	A	18: 13,002,074 (GRCm39)		probably benign	Het
Pcdh17	T	C	14: 84,685,084 (GRCm39)	V517A	possibly damaging	Het
Pcdhb14	T	A	18: 37,583,157 (GRCm39)	C754*	probably null	Het
Pkd1	T	C	17: 24,791,988 (GRCm39)	V1225A	probably damaging	Het
Plekhm3	T	C	1: 64,960,802 (GRCm39)	N485D	probably benign	Het
Plekho1	A	C	3: 95,902,995 (GRCm39)	S14A	unknown	Het
Ppp2r3d	A	T	9: 101,090,006 (GRCm39)	C106S	probably benign	Het
Ppp6c	A	C	2: 39,094,928 (GRCm39)	L99R	probably damaging	Het
Pramel27	A	G	4: 143,578,345 (GRCm39)	S202G	probably benign	Het
Prkdc	T	A	16: 15,653,091 (GRCm39)	Y3855*	probably null	Het
Ptpru	A	T	4: 131,503,565 (GRCm39)	I1155N	possibly damaging	Het
Reln	C	T	5: 22,216,059 (GRCm39)	G1042D	probably damaging	Het
Sall4	A	G	2: 168,596,773 (GRCm39)	V689A	probably benign	Het
Sec31b	C	T	19: 44,507,741 (GRCm39)	G768S	probably damaging	Het
Serpinb10	T	A	1: 107,474,549 (GRCm39)	V237D	probably benign	Het
Serpinb9	T	G	13: 33,199,579 (GRCm39)	D291E	probably benign	Het
Slc12a7	T	G	13: 73,954,089 (GRCm39)		probably benign	Het
Slfn8	A	T	11: 82,907,902 (GRCm39)	F214I	probably damaging	Het
Slu7	A	T	11: 43,328,952 (GRCm39)	D58V	probably damaging	Het
Smu1	T	C	4: 40,745,558 (GRCm39)	Y254C	probably damaging	Het
Snapc4	A	T	2: 26,260,805 (GRCm39)	Y479*	probably null	Het
Spopfm1	A	C	3: 94,173,153 (GRCm39)	S50R	possibly damaging	Het
Tbck	T	C	3: 132,428,130 (GRCm39)		probably null	Het
Tcf7l1	T	C	6: 72,610,259 (GRCm39)	Y246C	probably damaging	Het
Tmem43	C	T	6: 91,463,897 (GRCm39)	R391W	possibly damaging	Het
Trav7-1	T	G	14: 52,892,566 (GRCm39)	S40A	possibly damaging	Het
Trim45	T	A	3: 100,832,440 (GRCm39)	Y224*	probably null	Het
Trio	A	T	15: 27,852,097 (GRCm39)	I798N	possibly damaging	Het
Trnau1ap	A	T	4: 132,056,662 (GRCm39)		probably null	Het
Vmn1r213	T	C	13: 23,196,043 (GRCm39)	S209P	probably damaging	Het
Ythdf1	G	T	2: 180,552,857 (GRCm39)	R453S	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
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
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'- TCTAAAGAGCTGCTTTGTCGTTTTC -3'
(R):5'- TTAAGGTTACCCTGCTGAAAGATC -3'

Sequencing Primer
(F):5'- GTCGTTTTCTTTTCAACATGATGC -3'
(R):5'- AGACTGTGTTCCTAGTACTAGCAGAG -3'

Posted On

2021-11-19