Mutagenetix > Incidental Mutation

Incidental Mutation 'R7340:Sema4d'

569794

Institutional Source

Beutler Lab

Gene Symbol

Sema4d

Ensembl Gene

ENSMUSG00000021451

Gene Name

sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D

Synonyms

Semacl2, Semcl2, Semaj, M-sema G, coll-4, CD100, semaphorin H

MMRRC Submission

045430-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7340 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

51839565-51947783 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 51877598 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 78 (I78N)

Ref Sequence

ENSEMBL: ENSMUSP00000021900 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021900] [ENSMUST00000110039] [ENSMUST00000110040]

AlphaFold

O09126

Predicted Effect

probably damaging
Transcript: ENSMUST00000021900
AA Change: I78N

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

SMART Domains

Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
AA Change: I78N

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
Sema	50	482	7.68e-192	SMART
PSI	502	554	1.41e-12	SMART
IG	561	647	4.78e-1	SMART
transmembrane domain	733	755	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000110039
AA Change: I78N

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

SMART Domains

Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
AA Change: I78N

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
Sema	50	482	7.68e-192	SMART
PSI	502	554	1.41e-12	SMART
IG	561	647	4.78e-1	SMART
transmembrane domain	733	755	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000110040
AA Change: I78N

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

SMART Domains

Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
AA Change: I78N

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
Sema	50	482	7.68e-192	SMART
PSI	502	554	1.41e-12	SMART
IG	561	647	4.78e-1	SMART
transmembrane domain	733	755	N/A	INTRINSIC

Meta Mutation Damage Score

0.6416

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

99% (83/84)

MGI Phenotype

PHENOTYPE: Mice homozygous for disruptions in this gene display functional defects in their immune system but are normal in other systems of the body. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb11	C	T	2: 69,130,211 (GRCm39)	D282N	probably damaging	Het
Adam30	A	T	3: 98,069,637 (GRCm39)	N490I	probably benign	Het
Ankrd55	A	T	13: 112,492,497 (GRCm39)	I223F	probably damaging	Het
Ano8	T	A	8: 71,935,655 (GRCm39)	E321V	probably damaging	Het
Apc2	A	G	10: 80,149,316 (GRCm39)	K1457E	probably benign	Het
Asb15	T	A	6: 24,558,513 (GRCm39)	V38E	probably benign	Het
Atp4a	T	C	7: 30,416,155 (GRCm39)	S417P	possibly damaging	Het
AY358078	A	G	14: 52,063,716 (GRCm39)	N454S	probably damaging	Het
Cables2	A	G	2: 179,903,450 (GRCm39)	Y245H		Het
Cactin	CCGGAGTCGGAGTCGGAGTCGGAGTCGGAGTCGGAG	CCGGAGTCGGAGTCGGAGTCGGAGTCGGAGTCGGAGTCGGAG	10: 81,157,152 (GRCm39)		probably benign	Het
Camsap3	G	A	8: 3,637,960 (GRCm39)		probably null	Het
Ccdc178	A	T	18: 22,150,518 (GRCm39)	V705E	probably benign	Het
Ccdc47	T	C	11: 106,091,799 (GRCm39)	Q472R	possibly damaging	Het
Ccdc62	A	G	5: 124,089,283 (GRCm39)	D307G	probably damaging	Het
Cdcp3	A	G	7: 130,879,344 (GRCm39)	T1788A	unknown	Het
Cdh23	A	G	10: 60,366,775 (GRCm39)	I235T	probably benign	Het
Cep89	G	A	7: 35,129,353 (GRCm39)	R630H	probably damaging	Het
Cfap65	T	C	1: 74,960,742 (GRCm39)	N743D	probably benign	Het
Cimap1b	T	A	15: 89,262,610 (GRCm39)	T116S	probably benign	Het
Clec16a	A	G	16: 10,398,827 (GRCm39)	N329S	probably null	Het
Col25a1	A	G	3: 130,340,006 (GRCm39)		probably null	Het
Daam1	T	G	12: 72,035,713 (GRCm39)	D969E	probably benign	Het
Dntt	A	C	19: 41,047,004 (GRCm39)		probably null	Het
Dsel	C	T	1: 111,789,303 (GRCm39)	G411S	probably damaging	Het
Dst	T	A	1: 34,229,810 (GRCm39)	Y2468N	probably benign	Het
Exosc9	A	G	3: 36,615,297 (GRCm39)	T262A	possibly damaging	Het
Exph5	G	A	9: 53,288,309 (GRCm39)	A1797T	probably damaging	Het
Fbp2	A	T	13: 62,985,061 (GRCm39)	Y287N	probably damaging	Het
Fmn2	CCCTCCTCTCCCTGGAATGGGAATACCTCCCCCACCTCCTCTCCCTGGAATGGGAATACCTCCCCCACCTCCTCTCCCTGGAATGGGAATATCTCCCCTACCTCCTCTCCCTGGAATGGGAATACCTCC	CCCTCCTCTCCCTGGAATGGGAATACCTCCCCCACCTCCTCTCCCTGGAATGGGAATATCTCCCCTACCTCCTCTCCCTGGAATGGGAATACCTCC	1: 174,436,769 (GRCm39)		probably benign	Het
Fus	T	A	7: 127,581,123 (GRCm39)		probably null	Het
Galnt9	T	A	5: 110,762,054 (GRCm39)	N397K	probably damaging	Het
Gdi1	G	A	X: 73,350,461 (GRCm39)	R55H	probably benign	Het
Gga1	A	G	15: 78,775,651 (GRCm39)	T369A	probably benign	Het
Gp1ba	T	C	11: 70,531,119 (GRCm39)	I295T	unknown	Het
Hk2	T	C	6: 82,705,873 (GRCm39)	E810G	probably benign	Het
Igsf10	A	G	3: 59,233,189 (GRCm39)	V1848A	probably damaging	Het
Insrr	G	A	3: 87,721,623 (GRCm39)		probably null	Het
Ip6k3	T	A	17: 27,367,504 (GRCm39)	M231L	probably benign	Het
Itgb8	T	C	12: 119,155,939 (GRCm39)	N171S	probably benign	Het
Ldlrad3	T	C	2: 101,897,184 (GRCm39)		probably null	Het
Ltbp1	T	A	17: 75,634,223 (GRCm39)	C886*	probably null	Het
Mettl13	T	C	1: 162,366,547 (GRCm39)	D444G	probably benign	Het
Mns1	A	G	9: 72,356,025 (GRCm39)	Y224C	probably damaging	Het
Mri1	C	T	8: 84,983,525 (GRCm39)	R122Q	probably benign	Het
Ms4a6d	G	A	19: 11,567,437 (GRCm39)	Q155*	probably null	Het
Myo5c	A	C	9: 75,196,423 (GRCm39)	K1290Q	probably benign	Het
Nlrp12	T	G	7: 3,281,755 (GRCm39)	Q842H	possibly damaging	Het
Oga	G	A	19: 45,755,895 (GRCm39)	Q583*	probably null	Het
Or14c44	T	C	7: 86,061,957 (GRCm39)	L129P	possibly damaging	Het
Or14j8	T	A	17: 38,263,413 (GRCm39)	R167S	probably benign	Het
Or2t1	A	T	14: 14,328,401 (GRCm38)	T97S	possibly damaging	Het
Or5d39	T	C	2: 87,979,620 (GRCm39)	T248A	possibly damaging	Het
Otoa	A	G	7: 120,729,288 (GRCm39)	T554A	probably benign	Het
Per1	A	G	11: 68,994,008 (GRCm39)	D438G	probably damaging	Het
Phactr3	G	A	2: 177,975,854 (GRCm39)	R533H	probably damaging	Het
Phykpl	T	C	11: 51,490,370 (GRCm39)	F417S	probably damaging	Het
Pole	A	T	5: 110,482,330 (GRCm39)	T2057S	probably benign	Het
Polq	A	G	16: 36,881,288 (GRCm39)	T1151A	probably benign	Het
Polr1g	T	C	7: 19,093,073 (GRCm39)	T36A	probably benign	Het
Rbm26	A	T	14: 105,389,976 (GRCm39)	V216E	possibly damaging	Het
Ryk	T	C	9: 102,775,737 (GRCm39)	I449T	probably damaging	Het
Sap25	A	G	5: 137,640,935 (GRCm39)	T225A	probably benign	Het
Sart3	A	G	5: 113,882,728 (GRCm39)	M864T	probably benign	Het
Sec31b	T	C	19: 44,517,161 (GRCm39)	S280G	probably benign	Het
Sgip1	G	C	4: 102,778,661 (GRCm39)	R419S	unknown	Het
Slc13a3	T	C	2: 165,272,210 (GRCm39)	I278V	probably benign	Het
Slc2a5	A	G	4: 150,224,439 (GRCm39)	D312G	probably benign	Het
Slc39a2	A	T	14: 52,131,660 (GRCm39)	Q77L	possibly damaging	Het
Srbd1	A	T	17: 86,443,782 (GRCm39)	V148E	probably benign	Het
Syngr2	A	G	11: 117,703,322 (GRCm39)	E46G	probably damaging	Het
Taok1	A	G	11: 77,470,643 (GRCm39)	V54A	possibly damaging	Het
Tas2r106	T	A	6: 131,655,185 (GRCm39)	H222L	probably damaging	Het
Tcaf3	A	G	6: 42,566,848 (GRCm39)	I747T	probably benign	Het
Tmem151b	G	T	17: 45,856,195 (GRCm39)	P415Q	probably benign	Het
Tmf1	T	C	6: 97,145,061 (GRCm39)	D659G	possibly damaging	Het
Tnn	G	T	1: 159,973,592 (GRCm39)	D258E	probably damaging	Het
Traj33	A	G	14: 54,422,862 (GRCm39)	I16V	unknown	Het
Ttll13	G	T	7: 79,906,772 (GRCm39)	C480F	probably damaging	Het
Ttn	T	C	2: 76,714,415 (GRCm39)	N8137S	unknown	Het
Vmn1r85	T	C	7: 12,819,073 (GRCm39)	N24D	probably damaging	Het
Wdr81	T	C	11: 75,335,525 (GRCm39)	Q649R	probably null	Het
Zan	T	C	5: 137,382,092 (GRCm39)	T5152A	unknown	Het
Zc3h6	A	G	2: 128,835,110 (GRCm39)	D82G	possibly damaging	Het

Other mutations in Sema4d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02131:Sema4d	APN	13	51,856,973 (GRCm39)	splice site	probably null
IGL02155:Sema4d	APN	13	51,857,303 (GRCm39)	missense	probably benign	0.01
IGL02422:Sema4d	APN	13	51,857,124 (GRCm39)	missense	probably benign
IGL02795:Sema4d	APN	13	51,857,447 (GRCm39)	missense	probably benign	0.00
IGL03068:Sema4d	APN	13	51,862,922 (GRCm39)	missense	probably damaging	1.00
IGL03164:Sema4d	APN	13	51,862,958 (GRCm39)	missense	possibly damaging	0.58
R0060:Sema4d	UTSW	13	51,859,293 (GRCm39)	unclassified	probably benign
R0060:Sema4d	UTSW	13	51,859,293 (GRCm39)	unclassified	probably benign
R0305:Sema4d	UTSW	13	51,866,764 (GRCm39)	missense	probably damaging	1.00
R0309:Sema4d	UTSW	13	51,879,347 (GRCm39)	missense	probably benign	0.14
R0708:Sema4d	UTSW	13	51,866,755 (GRCm39)	missense	probably benign	0.17
R1809:Sema4d	UTSW	13	51,867,727 (GRCm39)	critical splice donor site	probably null
R1851:Sema4d	UTSW	13	51,865,258 (GRCm39)	missense	possibly damaging	0.94
R2096:Sema4d	UTSW	13	51,864,037 (GRCm39)	missense	probably damaging	1.00
R2159:Sema4d	UTSW	13	51,874,571 (GRCm39)	missense	probably damaging	1.00
R2367:Sema4d	UTSW	13	51,857,176 (GRCm39)	intron	probably benign
R4329:Sema4d	UTSW	13	51,857,340 (GRCm39)	missense	probably benign
R4372:Sema4d	UTSW	13	51,866,767 (GRCm39)	missense	probably damaging	1.00
R4384:Sema4d	UTSW	13	51,856,919 (GRCm39)	missense	probably damaging	1.00
R4590:Sema4d	UTSW	13	51,877,654 (GRCm39)	missense	probably benign	0.29
R4980:Sema4d	UTSW	13	51,865,270 (GRCm39)	missense	probably damaging	1.00
R5523:Sema4d	UTSW	13	51,865,390 (GRCm39)	missense	possibly damaging	0.89
R6086:Sema4d	UTSW	13	51,867,781 (GRCm39)	missense	probably damaging	1.00
R7197:Sema4d	UTSW	13	51,856,872 (GRCm39)	missense	probably benign	0.01
R7606:Sema4d	UTSW	13	51,877,658 (GRCm39)	missense	probably benign	0.00
R7859:Sema4d	UTSW	13	51,876,387 (GRCm39)	missense	probably benign	0.30
R8193:Sema4d	UTSW	13	51,859,192 (GRCm39)	nonsense	probably null
R8703:Sema4d	UTSW	13	51,854,959 (GRCm39)	missense
R8796:Sema4d	UTSW	13	51,865,546 (GRCm39)	missense	probably damaging	1.00
R8842:Sema4d	UTSW	13	51,863,018 (GRCm39)	missense	probably benign	0.04
R8904:Sema4d	UTSW	13	51,854,935 (GRCm39)	nonsense	probably null
R9016:Sema4d	UTSW	13	51,867,794 (GRCm39)	missense	probably damaging	1.00
R9115:Sema4d	UTSW	13	51,877,596 (GRCm39)	missense	probably benign
Z1176:Sema4d	UTSW	13	51,857,111 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- TGAATTTCAGATGTCCTCAGCCTC -3'
(R):5'- CTGAGTTCTGCTCCATGCTG -3'

Sequencing Primer
(F):5'- AGATGTCCTCAGCCTCCATTAC -3'
(R):5'- CACGCAGGCTCAGCAGTG -3'

Posted On

2019-09-13