Mutagenetix > Incidental Mutations

Incidental Mutation 'R4384:Sema4d'

326128

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

MMRRC Submission

042002-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4384 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

51685529-51793747 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 51702883 bp

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 771 (L771P)

Ref Sequence

ENSEMBL: ENSMUSP00000105667 (fasta)

Gene Model

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000021900
AA Change: L771P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
AA Change: L771P

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: L771P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
AA Change: L771P

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: L771P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
AA Change: L771P

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

0.4127

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.4%

Validation Efficiency

97% (56/58)

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acer2	T	A	4: 86,874,568	V27E	possibly damaging	Het
Adam23	T	C	1: 63,566,628	Y624H	probably damaging	Het
Arhgef10	T	A	8: 14,930,157	C132*	probably null	Het
Boc	A	T	16: 44,491,182	L726H	probably damaging	Het
Brip1	A	T	11: 86,148,429	D426E	possibly damaging	Het
Cadps2	T	A	6: 23,412,988	Q654L	probably benign	Het
Calr3	T	A	8: 72,428,164	D120V	probably damaging	Het
Cntnap3	A	G	13: 64,748,460	Y1067H	probably damaging	Het
Csnk1g1	T	C	9: 66,019,908	V119A	probably damaging	Het
Ddias	G	A	7: 92,858,223	T828I	probably damaging	Het
Dennd4c	A	G	4: 86,811,450	Y763C	probably damaging	Het
Dscam	T	A	16: 96,709,216	I948F	probably damaging	Het
E030018B13Rik	A	G	7: 63,919,393		probably benign	Het
E2f8	G	A	7: 48,867,099	T844I	possibly damaging	Het
Eps8	T	A	6: 137,499,592	H603L	probably benign	Het
Esrrg	G	A	1: 188,043,711	C122Y	probably damaging	Het
Frmd4a	C	T	2: 4,594,563	R467*	probably null	Het
Gad2	G	A	2: 22,685,410	V509I	probably benign	Het
Gpat4	A	G	8: 23,174,586	I446T	probably benign	Het
Klhl12	T	G	1: 134,487,654	D435E	probably damaging	Het
Luc7l	T	C	17: 26,279,962		probably benign	Het
March2	C	A	17: 33,696,193	M142I	probably benign	Het
Marf1	T	A	16: 14,142,641	Y513F	possibly damaging	Het
Mdm2	T	C	10: 117,696,439	D114G	possibly damaging	Het
Med1	G	A	11: 98,152,862		probably benign	Het
Meikin	C	T	11: 54,417,787	Q404*	probably null	Het
Myh9	A	T	15: 77,791,712		probably benign	Het
Mylip	T	C	13: 45,389,958	M1T	probably null	Het
Ncapg2	T	C	12: 116,439,877		probably null	Het
Nmd3	T	C	3: 69,724,398		probably benign	Het
Nwd2	T	A	5: 63,806,571	L1166H	probably damaging	Het
Olfr341	A	G	2: 36,479,998	L44P	probably damaging	Het
Olfr912	T	C	9: 38,582,053	Y259H	probably damaging	Het
Rubcn	A	G	16: 32,856,902	I71T	probably damaging	Het
Rwdd3	T	C	3: 121,158,757		probably benign	Het
Ryr2	T	C	13: 11,605,233	E3826G	probably damaging	Het
Sdad1	T	C	5: 92,298,257	Q273R	probably benign	Het
Sdha	A	T	13: 74,326,985	I579K	possibly damaging	Het
Shroom3	G	T	5: 92,943,086	V1151F	probably damaging	Het
Slc6a11	A	G	6: 114,247,727	E624G	possibly damaging	Het
Tada3	G	T	6: 113,370,379	R117S	probably damaging	Het
Tm9sf3	T	C	19: 41,247,933	M130V	probably damaging	Het
Trpc1	C	A	9: 95,732,108	M34I	probably benign	Het
Trpc4ap	A	G	2: 155,640,507	V521A	possibly damaging	Het
Trpm2	A	G	10: 77,917,725	V1315A	probably benign	Het
Tvp23a	A	G	16: 10,428,682	S80P	probably benign	Het
Usp54	A	T	14: 20,550,085		probably null	Het
Vmn2r27	A	G	6: 124,224,156	Y281H	probably benign	Het
Vwf	T	A	6: 125,655,116	I37N	unknown	Het
Zfp329	G	A	7: 12,811,657		probably benign	Het
Zfp616	G	T	11: 74,083,179	L91F	possibly damaging	Het

Other mutations in Sema4d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02131:Sema4d	APN	13	51702937	intron	probably null
IGL02155:Sema4d	APN	13	51703267	missense	probably benign	0.01
IGL02422:Sema4d	APN	13	51703088	missense	probably benign
IGL02795:Sema4d	APN	13	51703411	missense	probably benign	0.00
IGL03068:Sema4d	APN	13	51708886	missense	probably damaging	1.00
IGL03164:Sema4d	APN	13	51708922	missense	possibly damaging	0.58
R0060:Sema4d	UTSW	13	51705257	unclassified	probably benign
R0060:Sema4d	UTSW	13	51705257	unclassified	probably benign
R0305:Sema4d	UTSW	13	51712728	missense	probably damaging	1.00
R0309:Sema4d	UTSW	13	51725311	missense	probably benign	0.14
R0708:Sema4d	UTSW	13	51712719	missense	probably benign	0.17
R1809:Sema4d	UTSW	13	51713691	critical splice donor site	probably null
R1851:Sema4d	UTSW	13	51711222	missense	possibly damaging	0.94
R2096:Sema4d	UTSW	13	51710001	missense	probably damaging	1.00
R2159:Sema4d	UTSW	13	51720535	missense	probably damaging	1.00
R2367:Sema4d	UTSW	13	51703140	intron	probably benign
R4329:Sema4d	UTSW	13	51703304	missense	probably benign
R4372:Sema4d	UTSW	13	51712731	missense	probably damaging	1.00
R4590:Sema4d	UTSW	13	51723618	missense	probably benign	0.29
R4980:Sema4d	UTSW	13	51711234	missense	probably damaging	1.00
R5523:Sema4d	UTSW	13	51711354	missense	possibly damaging	0.89
R6086:Sema4d	UTSW	13	51713745	missense	probably damaging	1.00
R7197:Sema4d	UTSW	13	51702836	missense	probably benign	0.01
R7340:Sema4d	UTSW	13	51723562	missense	probably damaging	1.00
R7606:Sema4d	UTSW	13	51723622	missense	probably benign	0.00
R7859:Sema4d	UTSW	13	51722351	missense	probably benign	0.30
R7942:Sema4d	UTSW	13	51722351	missense	probably benign	0.30
R7977:Sema4d	UTSW	13	51710006	missense	probably benign	0.40

Predicted Primers

PCR Primer
(F):5'- TTGACATCAAACGGTTTGTCC -3'
(R):5'- ATGGTCATCAACACGGTCCC -3'

Sequencing Primer
(F):5'- CAGAGAGTTCATCGATCCGTTGC -3'
(R):5'- GTCCCCCAGCTCCACTCAG -3'

Posted On

2015-07-06