Mutagenetix > Incidental Mutation

Incidental Mutation 'R8904:Sema4d'

678390

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

068761-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8904 (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 51854935 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Stop codon at position 54 (L54*)

Ref Sequence

ENSEMBL: ENSMUSP00000105669 (fasta)

Gene Model

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

AlphaFold

O09126

Predicted Effect

probably benign
Transcript: ENSMUST00000021900

SMART Domains

Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451

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: ENSMUST00000110039

SMART Domains

Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451

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: ENSMUST00000110040

SMART Domains

Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451

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: ENSMUST00000110042
AA Change: L54*

SMART Domains

Protein: ENSMUSP00000105669
Gene: ENSMUSG00000021451
AA Change: L54*

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

99% (66/67)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510009E07Rik	CCGGAAGGGGAGGAGCAGTGACCCAGTTTCGGA	CCGGA	16: 21,472,148 (GRCm39)		probably null	Het
Adcy1	T	G	11: 7,059,075 (GRCm39)	L327R	probably damaging	Het
Ajm1	A	T	2: 25,467,914 (GRCm39)	S666T	probably benign	Het
Amotl1	T	C	9: 14,469,861 (GRCm39)	Q624R	probably damaging	Het
Ampd1	A	G	3: 102,988,374 (GRCm39)	T106A	probably benign	Het
Aqr	T	A	2: 113,967,474 (GRCm39)	I514F	probably damaging	Het
Atp2b1	A	G	10: 98,804,866 (GRCm39)	T30A	possibly damaging	Het
Atp9a	A	T	2: 168,547,097 (GRCm39)	Y186N	probably benign	Het
Bub1	T	A	2: 127,671,622 (GRCm39)	N21I	possibly damaging	Het
Cachd1	G	A	4: 100,810,363 (GRCm39)	D322N	probably damaging	Het
Ccdc38	A	G	10: 93,411,197 (GRCm39)	E402G	probably damaging	Het
Ccl27a	A	T	4: 41,774,194 (GRCm39)		probably null	Het
Clec4a4	T	C	6: 122,990,836 (GRCm39)		probably benign	Het
Clic5	A	T	17: 44,552,992 (GRCm39)	K82M	probably benign	Het
Cnot10	A	T	9: 114,430,423 (GRCm39)	S566T	probably benign	Het
Cul9	T	C	17: 46,831,427 (GRCm39)	T1596A	probably damaging	Het
Cyp2c55	A	G	19: 39,022,816 (GRCm39)	E318G		Het
Entpd8	A	C	2: 24,973,575 (GRCm39)		probably benign	Het
Epb41l5	A	G	1: 119,547,936 (GRCm39)	F156L	probably damaging	Het
Ephb4	T	A	5: 137,369,067 (GRCm39)	M819K	probably damaging	Het
Esr1	A	G	10: 4,696,654 (GRCm39)	R168G	possibly damaging	Het
Fbxw10	C	A	11: 62,765,831 (GRCm39)	Y700*	probably null	Het
Fras1	G	T	5: 96,929,138 (GRCm39)	R3847S	probably benign	Het
Gm11110	T	C	17: 57,410,439 (GRCm39)	T20A	unknown	Het
Gpr150	G	T	13: 76,204,528 (GRCm39)	S139*	probably null	Het
Grm1	A	T	10: 10,595,281 (GRCm39)	N782K	probably damaging	Het
Hmcn2	A	G	2: 31,323,404 (GRCm39)	S4173G	possibly damaging	Het
Hmx1	T	A	5: 35,549,511 (GRCm39)	V268D	probably damaging	Het
Hsbp1l1	T	C	18: 80,278,685 (GRCm39)	T33A	possibly damaging	Het
Hsd17b3	T	C	13: 64,212,194 (GRCm39)	T161A	probably damaging	Het
Igll1	A	T	16: 16,681,576 (GRCm39)	W60R	probably benign	Het
Itga11	A	G	9: 62,664,893 (GRCm39)	T593A	probably benign	Het
Kat6a	A	G	8: 23,428,824 (GRCm39)	D1393G	possibly damaging	Het
Krt36	A	G	11: 99,996,173 (GRCm39)	F84L	probably benign	Het
Macrod1	T	C	19: 7,174,385 (GRCm39)	S266P	probably damaging	Het
Mib2	A	G	4: 155,744,173 (GRCm39)	V163A	probably damaging	Het
Mmut	A	G	17: 41,248,284 (GRCm39)	T104A	probably damaging	Het
Mpl	A	G	4: 118,301,263 (GRCm39)	L534P		Het
Myo3b	C	A	2: 70,257,252 (GRCm39)	H1317N	probably benign	Het
Nkx2-6	A	G	14: 69,409,420 (GRCm39)	D57G	probably benign	Het
Or1ab2	A	G	8: 72,864,276 (GRCm39)	I289V	probably damaging	Het
Or5b24	T	C	19: 12,912,192 (GRCm39)	V30A	probably benign	Het
Or5d46	T	G	2: 88,169,949 (GRCm39)	F13L	possibly damaging	Het
Or5p79	A	G	7: 108,221,919 (GRCm39)	N300S	probably damaging	Het
Or6s1	A	G	14: 51,308,665 (GRCm39)	Y62H	probably damaging	Het
Or7g33	A	T	9: 19,448,760 (GRCm39)	D155E	possibly damaging	Het
Osbpl11	T	A	16: 33,047,607 (GRCm39)	H523Q	probably damaging	Het
Pde1c	A	T	6: 56,156,128 (GRCm39)	S148T	possibly damaging	Het
Pign	G	A	1: 105,519,359 (GRCm39)	A521V	possibly damaging	Het
Pprc1	A	G	19: 46,060,183 (GRCm39)	M1536V	possibly damaging	Het
Prg4	C	A	1: 150,331,810 (GRCm39)	A288S	possibly damaging	Het
Prim2	A	T	1: 33,669,513 (GRCm39)	I154N	possibly damaging	Het
Prkdc	T	C	16: 15,545,590 (GRCm39)	V1902A	probably benign	Het
Prss40	C	T	1: 34,595,045 (GRCm39)		probably benign	Het
Ret	C	T	6: 118,157,174 (GRCm39)		probably benign	Het
Rgs22	A	T	15: 36,026,127 (GRCm39)	C1056S	probably damaging	Het
Schip1	T	C	3: 68,402,436 (GRCm39)	L199P	possibly damaging	Het
Sgsm1	C	T	5: 113,421,495 (GRCm39)	G531R	probably benign	Het
Tas1r2	T	C	4: 139,394,714 (GRCm39)	F519S	probably damaging	Het
Tnfsf11	C	T	14: 78,516,119 (GRCm39)	R283Q	possibly damaging	Het
Tril	C	T	6: 53,797,202 (GRCm39)	V7M	possibly damaging	Het
Tsr1	T	A	11: 74,790,217 (GRCm39)	Y137*	probably null	Het
Ubr5	A	G	15: 38,042,153 (GRCm39)	S148P		Het
Unc13b	A	G	4: 43,178,531 (GRCm39)		probably benign	Het
Zfp606	A	G	7: 12,223,506 (GRCm39)	T64A	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
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
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'- TGTACCTTTACGGCGAGAGG -3'
(R):5'- GACGACTTCTTCCTCAGTGC -3'

Sequencing Primer
(F):5'- AGCCCTAGCAACAGCGTTG -3'
(R):5'- AGTGCCTTCTTTTGTGTCCTCTG -3'

Posted On

2021-08-02