Mutagenetix > Incidental Mutation

Incidental Mutation 'R8193:Sema4d'

635312

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

067616-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8193 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

51839565-51947783 bp(-) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

A to T at 51859192 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Stop codon at position 512 (C512*)

Ref Sequence

ENSEMBL: ENSMUSP00000021900 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021900] [ENSMUST00000110039] [ENSMUST00000110040] [ENSMUST00000110042]

AlphaFold

O09126

Predicted Effect

probably null
Transcript: ENSMUST00000021900
AA Change: C512*

SMART Domains

Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
AA Change: C512*

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 null
Transcript: ENSMUST00000110039
AA Change: C512*

SMART Domains

Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
AA Change: C512*

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 null
Transcript: ENSMUST00000110040
AA Change: C512*

SMART Domains

Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
AA Change: C512*

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 benign
Transcript: ENSMUST00000110042

SMART Domains

Protein: ENSMUSP00000105669
Gene: ENSMUSG00000021451

Domain	Start	End	E-Value	Type
Blast:IG	2	46	2e-15	BLAST

Meta Mutation Damage Score

0.9756

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.4%

Validation Efficiency

98% (62/63)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	A	T	3: 124,213,517 (GRCm39)	V48E	possibly damaging	Het
4930522H14Rik	A	G	4: 109,381,529 (GRCm39)	L83S	probably benign	Het
Abhd18	C	A	3: 40,884,660 (GRCm39)	T233K	probably benign	Het
Adam26a	A	T	8: 44,022,273 (GRCm39)	C406S	probably damaging	Het
Anp32e	G	A	3: 95,836,710 (GRCm39)		probably benign	Het
Cd33	C	T	7: 43,181,696 (GRCm39)	A155T	possibly damaging	Het
Cdc25c	A	T	18: 34,882,675 (GRCm39)		probably null	Het
Cep350	A	G	1: 155,737,825 (GRCm39)	S2673P	probably benign	Het
Chodl	T	C	16: 78,738,412 (GRCm39)	S127P	probably damaging	Het
Clstn2	A	G	9: 97,465,683 (GRCm39)	S103P	probably damaging	Het
Crocc2	T	A	1: 93,117,888 (GRCm39)		probably null	Het
Cyp24a1	A	G	2: 170,327,622 (GRCm39)	L507P	probably damaging	Het
Dcbld2	T	A	16: 58,284,373 (GRCm39)		probably null	Het
Dnah14	T	C	1: 181,515,770 (GRCm39)	Y1991H	probably damaging	Het
Dnajb8	C	T	6: 88,199,940 (GRCm39)	R159C	possibly damaging	Het
Edrf1	C	T	7: 133,263,606 (GRCm39)	T971I	possibly damaging	Het
Ermap	A	G	4: 119,041,140 (GRCm39)	I290T	possibly damaging	Het
Eva1a	A	T	6: 82,068,921 (GRCm39)	S83C	probably benign	Het
Fcgbp	A	T	7: 27,804,276 (GRCm39)	N1795Y	probably damaging	Het
Foxg1	A	G	12: 49,432,377 (GRCm39)	H370R	possibly damaging	Het
Gabra1	A	G	11: 42,037,968 (GRCm39)	Y217H	probably damaging	Het
Gm3086	A	G	12: 70,016,264 (GRCm39)	N62S	noncoding transcript	Het
Hmcn1	A	T	1: 150,453,228 (GRCm39)	Y5362*	probably null	Het
Igkv5-37	C	A	6: 69,940,796 (GRCm39)		probably benign	Het
Ints3	A	G	3: 90,307,929 (GRCm39)	V647A	possibly damaging	Het
Itga1	A	G	13: 115,104,991 (GRCm39)		probably null	Het
Limk2	T	C	11: 3,297,691 (GRCm39)	K481E	possibly damaging	Het
Lonp2	G	T	8: 87,358,091 (GRCm39)	G104V	probably damaging	Het
Lpar5	T	C	6: 125,058,302 (GRCm39)	S8P	probably benign	Het
Map2k7	T	C	8: 4,294,059 (GRCm39)	F202L	probably benign	Het
Mark1	T	G	1: 184,660,249 (GRCm39)	M136L	probably damaging	Het
Myo15b	T	C	11: 115,775,973 (GRCm39)	S590P	probably damaging	Het
Nbas	T	C	12: 13,483,010 (GRCm39)	V1429A	probably damaging	Het
Nbeal1	T	A	1: 60,292,640 (GRCm39)	Y1097*	probably null	Het
Ncf4	T	C	15: 78,146,466 (GRCm39)	S299P	probably damaging	Het
Nfkbiz	T	C	16: 55,642,214 (GRCm39)	D68G	probably damaging	Het
Nomo1	T	C	7: 45,692,037 (GRCm39)	S154P	possibly damaging	Het
Nrp1	G	T	8: 129,187,187 (GRCm39)	W411L	probably damaging	Het
Or10d1b	T	C	9: 39,613,498 (GRCm39)	D189G	possibly damaging	Het
Or4c105	T	A	2: 88,647,803 (GRCm39)	M96K	probably damaging	Het
Or5t18	T	G	2: 86,637,209 (GRCm39)	I45L	noncoding transcript	Het
Or8g2b	T	C	9: 39,750,757 (GRCm39)	I9T	probably benign	Het
Or9g4b	T	C	2: 85,616,305 (GRCm39)	V150A	probably benign	Het
Pcsk5	A	G	19: 17,563,415 (GRCm39)	V574A	possibly damaging	Het
Prex1	C	A	2: 166,435,780 (GRCm39)	R589L	possibly damaging	Het
Prl7d1	A	G	13: 27,893,230 (GRCm39)	V227A		Het
Prpf40b	T	A	15: 99,201,949 (GRCm39)	F16I	unknown	Het
Rasa2	G	A	9: 96,484,791 (GRCm39)	P141L	probably damaging	Het
Rtl1	A	G	12: 109,558,650 (GRCm39)	V1063A	probably benign	Het
Slc19a2	A	G	1: 164,084,794 (GRCm39)	N228S	probably benign	Het
Tcf4	A	T	18: 69,633,994 (GRCm39)		probably benign	Het
Tnks2	T	C	19: 36,832,353 (GRCm39)	V264A	possibly damaging	Het
Ugt2b35	T	A	5: 87,149,302 (GRCm39)	S184R	probably damaging	Het
Usp53	T	C	3: 122,741,012 (GRCm39)	E746G	probably benign	Het
Utp18	T	C	11: 93,766,903 (GRCm39)	D268G	probably damaging	Het
Vmn1r172	T	A	7: 23,359,752 (GRCm39)	Y212*	probably null	Het
Vmn2r100	T	A	17: 19,725,102 (GRCm39)	C10*	probably null	Het
Vmn2r113	G	T	17: 23,164,501 (GRCm39)	V135F	probably benign	Het
Vps54	T	C	11: 21,242,045 (GRCm39)	F387L	probably benign	Het
Xab2	A	C	8: 3,663,389 (GRCm39)	D450E	probably benign	Het
Zfp408	G	T	2: 91,475,361 (GRCm39)	R598S	probably benign	Het
Zfp788	T	A	7: 41,298,038 (GRCm39)	C225S	probably benign	Het
Zfp944	T	A	17: 22,558,861 (GRCm39)	K129*	probably null	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
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
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'- TCATGTCCTGAATCCAGCCC -3'
(R):5'- TCTGAGTCAGTGAGTCCTTCCC -3'

Sequencing Primer
(F):5'- GTCCTGAATCCAGCCCCTAGAAG -3'
(R):5'- ACTGTGCTGTCTTCCCAGGAG -3'

Posted On

2020-07-13