Mutagenetix > Incidental Mutation

Incidental Mutation 'R1851:Sema4d'

208128

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

039875-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1851 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

51839565-51947783 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 51865258 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 362 (V362A)

Ref Sequence

ENSEMBL: ENSMUSP00000105667 (fasta)

Gene Model

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

AlphaFold

O09126

Predicted Effect

possibly damaging
Transcript: ENSMUST00000021900
AA Change: V362A

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
AA Change: V362A

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

possibly damaging
Transcript: ENSMUST00000110039
AA Change: V362A

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
AA Change: V362A

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

possibly damaging
Transcript: ENSMUST00000110040
AA Change: V362A

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
AA Change: V362A

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

noncoding transcript
Transcript: ENSMUST00000125511

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 94.9%
20x: 91.3%

Validation Efficiency

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: 95 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5730507C01Rik	A	G	12: 18,583,687 (GRCm39)	E225G	possibly damaging	Het
Abcb7	T	C	X: 103,349,005 (GRCm39)	M153V	probably benign	Het
Abi1	A	T	2: 22,840,276 (GRCm39)	V329D	possibly damaging	Het
Ablim3	G	A	18: 61,982,466 (GRCm39)	H160Y	probably benign	Het
Acox3	A	T	5: 35,766,406 (GRCm39)	D624V	possibly damaging	Het
Adam6b	A	G	12: 113,455,442 (GRCm39)	D753G	probably benign	Het
Ago1	C	A	4: 126,333,788 (GRCm39)	R771L	probably benign	Het
Aktip	A	G	8: 91,852,505 (GRCm39)	V217A	possibly damaging	Het
Ankk1	A	C	9: 49,327,150 (GRCm39)	H676Q	probably benign	Het
Arl1	G	C	10: 88,569,408 (GRCm39)		probably benign	Het
Asxl3	T	A	18: 22,650,796 (GRCm39)	D928E	probably damaging	Het
AW209491	T	C	13: 14,811,318 (GRCm39)	V57A	possibly damaging	Het
B3galt4	G	T	17: 34,169,885 (GRCm39)	Q118K	probably benign	Het
Ccdc187	A	T	2: 26,166,080 (GRCm39)	M783K	probably benign	Het
Cdon	T	G	9: 35,394,454 (GRCm39)	M900R	probably damaging	Het
Ceacam5	G	A	7: 17,448,835 (GRCm39)	W67*	probably null	Het
Chd5	A	G	4: 152,462,727 (GRCm39)	S1356G	probably damaging	Het
Chil3	C	T	3: 106,056,117 (GRCm39)		probably null	Het
Chmp7	C	T	14: 69,956,899 (GRCm39)	M336I	probably benign	Het
Cntn1	C	T	15: 92,203,021 (GRCm39)	R768C	probably damaging	Het
Col6a3	T	A	1: 90,735,256 (GRCm39)	I798F	possibly damaging	Het
Cpxcr1	T	A	X: 115,387,758 (GRCm39)	L223*	probably null	Het
Cpz	C	A	5: 35,659,902 (GRCm39)	R581L	possibly damaging	Het
Cxcr2	A	G	1: 74,198,438 (GRCm39)	I311V	probably benign	Het
Cym	T	A	3: 107,126,030 (GRCm39)	I78F	probably benign	Het
Defb8	A	T	8: 19,495,899 (GRCm39)	S54T	probably benign	Het
Dennd4a	A	G	9: 64,769,312 (GRCm39)	T433A	probably damaging	Het
Dhx29	A	G	13: 113,084,815 (GRCm39)	T678A	probably damaging	Het
Dspp	T	C	5: 104,321,951 (GRCm39)		probably null	Het
Enkur	G	T	2: 21,193,988 (GRCm39)	A195E	probably benign	Het
Ero1b	T	A	13: 12,619,292 (GRCm39)	S429T	possibly damaging	Het
Fh1	A	G	1: 175,435,452 (GRCm39)	S344P	probably damaging	Het
Flnc	G	T	6: 29,443,478 (GRCm39)	G553V	probably damaging	Het
Fmo1	A	T	1: 162,657,554 (GRCm39)	L529*	probably null	Het
Frem1	C	A	4: 82,868,737 (GRCm39)	V1415F	probably damaging	Het
Gatb	T	G	3: 85,526,184 (GRCm39)	L354R	probably damaging	Het
Gdpgp1	A	T	7: 79,888,349 (GRCm39)	N127Y	probably damaging	Het
Gpat2	A	G	2: 127,276,739 (GRCm39)	T648A	possibly damaging	Het
Grk6	C	T	13: 55,599,591 (GRCm39)	R225*	probably null	Het
Hells	A	T	19: 38,948,120 (GRCm39)	Q682L	probably null	Het
Hspa5	T	A	2: 34,664,690 (GRCm39)	N381K	possibly damaging	Het
Ighmbp2	T	C	19: 3,312,075 (GRCm39)	N893S	probably benign	Het
Ipo11	A	T	13: 106,948,765 (GRCm39)	V914E	possibly damaging	Het
Lars1	T	C	18: 42,345,673 (GRCm39)	N1001S	probably benign	Het
Lats2	A	G	14: 57,934,912 (GRCm39)	L606P	probably damaging	Het
Map4k1	T	C	7: 28,699,209 (GRCm39)	Y521H	probably benign	Het
Marchf11	T	A	15: 26,387,916 (GRCm39)	V257E	probably damaging	Het
Med23	G	A	10: 24,786,768 (GRCm39)		probably null	Het
Meltf	A	G	16: 31,715,395 (GRCm39)	D696G	probably benign	Het
Ms4a7	T	A	19: 11,301,788 (GRCm39)	M212L	probably benign	Het
Mx1	A	T	16: 97,249,403 (GRCm39)	L608Q	probably damaging	Het
Myh1	T	C	11: 67,095,224 (GRCm39)	Y195H	probably damaging	Het
Napb	G	T	2: 148,548,909 (GRCm39)	H110Q	probably benign	Het
Ngly1	C	T	14: 16,260,585 (GRCm38)	P90S	probably damaging	Het
Nlrp1b	T	A	11: 71,073,442 (GRCm39)	I134L	possibly damaging	Het
Nup210	A	G	6: 90,993,036 (GRCm39)	L1017P	probably damaging	Het
Nup85	T	A	11: 115,472,643 (GRCm39)	I233N	probably damaging	Het
Obsl1	A	G	1: 75,469,537 (GRCm39)	V965A	probably damaging	Het
Or4c12	A	C	2: 89,774,158 (GRCm39)	Y100*	probably null	Het
Or4f6	T	C	2: 111,839,036 (GRCm39)	D165G	probably benign	Het
Or6c5c	T	C	10: 129,299,370 (GRCm39)	L275P	probably damaging	Het
Pak1ip1	A	G	13: 41,164,708 (GRCm39)	T264A	possibly damaging	Het
Pard6g	C	T	18: 80,160,357 (GRCm39)	R157C	probably damaging	Het
Pcdhb7	A	T	18: 37,475,631 (GRCm39)	T256S	possibly damaging	Het
Phrf1	T	C	7: 140,820,831 (GRCm39)	F153L	probably damaging	Het
Pigw	A	T	11: 84,768,874 (GRCm39)	F152I	probably damaging	Het
Pip4k2c	A	G	10: 127,036,744 (GRCm39)	S222P	probably damaging	Het
Pjvk	A	G	2: 76,487,775 (GRCm39)		probably null	Het
Plxnd1	C	T	6: 115,940,875 (GRCm39)	V1355M	probably damaging	Het
Pramel26	T	C	4: 143,539,396 (GRCm39)	I32M	probably benign	Het
Prss22	G	A	17: 24,215,288 (GRCm39)	P163S	probably damaging	Het
Prune2	A	G	19: 17,176,503 (GRCm39)	I154V	probably damaging	Het
Rapgef6	T	A	11: 54,533,637 (GRCm39)	D362E	probably benign	Het
Retreg2	A	G	1: 75,123,319 (GRCm39)	K416E	probably benign	Het
Scn7a	T	C	2: 66,510,635 (GRCm39)	I1256V	probably benign	Het
Septin4	T	A	11: 87,459,741 (GRCm39)	D496E	probably damaging	Het
Slc25a34	G	A	4: 141,349,579 (GRCm39)	T192I	probably benign	Het
Tacc3	G	T	5: 33,825,544 (GRCm39)	V425L	probably benign	Het
Tfdp2	A	T	9: 96,179,762 (GRCm39)	K125I	probably damaging	Het
Tjp2	C	T	19: 24,076,899 (GRCm39)	R952Q	possibly damaging	Het
Tk2	G	T	8: 104,975,077 (GRCm39)	S30*	probably null	Het
Tmem74	A	T	15: 43,730,559 (GRCm39)	D161E	probably benign	Het
Tmprss9	G	A	10: 80,728,119 (GRCm39)	V570M	probably damaging	Het
Tnk2	C	A	16: 32,498,280 (GRCm39)	P26Q	probably damaging	Het
Tnpo2	T	G	8: 85,778,401 (GRCm39)	V610G	probably damaging	Het
Trim37	T	C	11: 87,109,132 (GRCm39)	F953S	probably damaging	Het
U2surp	T	A	9: 95,364,150 (GRCm39)	K589*	probably null	Het
Usp2	G	A	9: 43,987,263 (GRCm39)	R187H	probably benign	Het
Vmn2r1	C	T	3: 64,008,926 (GRCm39)	T535I	probably benign	Het
Wdr20rt	T	A	12: 65,273,925 (GRCm39)	S463T	possibly damaging	Het
Zbtb25	C	A	12: 76,396,488 (GRCm39)	G245W	probably damaging	Het
Zc3h14	T	A	12: 98,726,613 (GRCm39)	L27*	probably null	Het
Zfp2	T	C	11: 50,791,915 (GRCm39)	K43E	probably benign	Het
Zfp268	T	G	4: 145,350,820 (GRCm39)		probably benign	Het
Zfp654	A	G	16: 64,605,491 (GRCm39)	Y904H	probably benign	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
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
R7340:Sema4d	UTSW	13	51,877,598 (GRCm39)	missense	probably damaging	1.00
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'- AGCTTCACTGTTCACCCCAG -3'
(R):5'- TTCACTTGTGAGTCCCTTGG -3'

Sequencing Primer
(F):5'- AGGCCCGGCAGCTACTC -3'
(R):5'- AGTTGGGGCCTGGTCAC -3'

Posted On

2014-06-23