Mutagenetix > Incidental Mutation

Incidental Mutation 'PIT4418001:Sema6c'

555566

Institutional Source

Beutler Lab

Gene Symbol

Sema6c

Ensembl Gene

ENSMUSG00000038777

Gene Name

sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C

Synonyms

Sema Y, Semay

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.303) question?

Stock #

PIT4418001 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

95067768-95081335 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 95077401 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 404 (D404E)

Ref Sequence

ENSEMBL: ENSMUSP00000088333 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000090821] [ENSMUST00000090823] [ENSMUST00000107217] [ENSMUST00000131620] [ENSMUST00000142449] [ENSMUST00000168321] [ENSMUST00000202315] [ENSMUST00000204709]

AlphaFold

Q9WTM3

Predicted Effect

probably damaging
Transcript: ENSMUST00000090821
AA Change: D404E

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000088331
Gene: ENSMUSG00000038777
AA Change: D404E

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
transmembrane domain	604	626	N/A	INTRINSIC
low complexity region	627	638	N/A	INTRINSIC
low complexity region	646	658	N/A	INTRINSIC
low complexity region	660	669	N/A	INTRINSIC
low complexity region	693	709	N/A	INTRINSIC
low complexity region	744	761	N/A	INTRINSIC
low complexity region	907	924	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000090823
AA Change: D404E

PolyPhen 2 Score 0.568 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000088333
Gene: ENSMUSG00000038777
AA Change: D404E

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
low complexity region	591	603	N/A	INTRINSIC
transmembrane domain	636	658	N/A	INTRINSIC
low complexity region	659	670	N/A	INTRINSIC
low complexity region	678	690	N/A	INTRINSIC
low complexity region	692	701	N/A	INTRINSIC
low complexity region	725	741	N/A	INTRINSIC
low complexity region	776	793	N/A	INTRINSIC
low complexity region	939	956	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000107217
AA Change: D364E

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000102835
Gene: ENSMUSG00000038777
AA Change: D364E

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	448	1.23e-126	SMART
low complexity region	551	563	N/A	INTRINSIC
transmembrane domain	596	618	N/A	INTRINSIC
low complexity region	619	630	N/A	INTRINSIC
low complexity region	638	650	N/A	INTRINSIC
low complexity region	652	661	N/A	INTRINSIC
low complexity region	685	701	N/A	INTRINSIC
low complexity region	736	753	N/A	INTRINSIC
low complexity region	899	916	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000131620

SMART Domains

Protein: ENSMUSP00000138154
Gene: ENSMUSG00000038777

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000142449

SMART Domains

Protein: ENSMUSP00000123457
Gene: ENSMUSG00000038777

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
low complexity region	591	603	N/A	INTRINSIC
transmembrane domain	636	658	N/A	INTRINSIC
low complexity region	659	670	N/A	INTRINSIC
low complexity region	678	690	N/A	INTRINSIC
low complexity region	692	701	N/A	INTRINSIC
low complexity region	725	741	N/A	INTRINSIC
low complexity region	776	793	N/A	INTRINSIC
low complexity region	939	956	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000168321
AA Change: D404E

PolyPhen 2 Score 0.568 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000129081
Gene: ENSMUSG00000038777
AA Change: D404E

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
transmembrane domain	604	626	N/A	INTRINSIC
low complexity region	627	638	N/A	INTRINSIC
low complexity region	646	658	N/A	INTRINSIC
low complexity region	660	669	N/A	INTRINSIC
low complexity region	693	709	N/A	INTRINSIC
low complexity region	744	761	N/A	INTRINSIC
low complexity region	907	924	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000202315
AA Change: D404E

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000144039
Gene: ENSMUSG00000038777
AA Change: D404E

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
transmembrane domain	604	626	N/A	INTRINSIC
low complexity region	627	638	N/A	INTRINSIC
low complexity region	646	658	N/A	INTRINSIC
low complexity region	660	669	N/A	INTRINSIC
low complexity region	693	709	N/A	INTRINSIC
low complexity region	744	761	N/A	INTRINSIC
low complexity region	907	924	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000204709

SMART Domains

Protein: ENSMUSP00000144702
Gene: ENSMUSG00000038777

Domain	Start	End	E-Value	Type
low complexity region	10	20	N/A	INTRINSIC
PDB:3OKY\|B	25	117	8e-8	PDB
Blast:Sema	62	119	9e-34	BLAST

Coding Region Coverage

1x: 93.3%
3x: 90.8%
10x: 84.7%
20x: 71.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010]
PHENOTYPE: Mice homozygous for a targeted mutation display a decrease in pain threshold. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abtb1	T	C	6: 88,816,630 (GRCm39)	Y100C	possibly damaging	Het
Adamtsl1	T	C	4: 86,161,961 (GRCm39)	Y365H	probably damaging	Het
Atad2b	A	T	12: 5,074,587 (GRCm39)	I1049F	probably benign	Het
Atg9b	A	T	5: 24,590,513 (GRCm39)	S859T	possibly damaging	Het
Banp	G	A	8: 122,732,365 (GRCm39)	A380T	probably damaging	Het
Brinp3	C	T	1: 146,777,161 (GRCm39)	T536I	probably damaging	Het
Cacna1c	T	C	6: 118,631,384 (GRCm39)	E1155G		Het
Capn12	T	C	7: 28,585,961 (GRCm39)	S270P	probably benign	Het
Cbs	A	T	17: 31,834,495 (GRCm39)	I498N	possibly damaging	Het
Cep68	T	C	11: 20,189,731 (GRCm39)	K427R	probably benign	Het
Cobl	G	A	11: 12,206,240 (GRCm39)	T545I	possibly damaging	Het
Cr2	T	A	1: 194,839,760 (GRCm39)	M556L	probably benign	Het
Crebbp	A	G	16: 3,932,689 (GRCm39)	S1068P	probably benign	Het
D2hgdh	C	T	1: 93,766,590 (GRCm39)	H385Y	possibly damaging	Het
Dennd1b	T	C	1: 139,008,999 (GRCm39)	L159P		Het
Dnajb4	A	T	3: 151,899,134 (GRCm39)	F31I	possibly damaging	Het
Dnajc16	A	G	4: 141,498,260 (GRCm39)	F369S	probably damaging	Het
Dtl	A	T	1: 191,273,429 (GRCm39)	L493H	possibly damaging	Het
Efcab5	T	A	11: 77,022,877 (GRCm39)	Q612L	possibly damaging	Het
Efr3b	A	T	12: 4,030,490 (GRCm39)	L407Q	possibly damaging	Het
Ehbp1	T	A	11: 22,003,494 (GRCm39)	Q1085L	probably damaging	Het
Ell	T	C	8: 71,034,331 (GRCm39)	V199A	probably damaging	Het
Elmod2	G	T	8: 84,048,171 (GRCm39)	T97K	probably benign	Het
Epn3	T	C	11: 94,386,956 (GRCm39)	E138G	probably damaging	Het
Esf1	A	T	2: 140,001,697 (GRCm39)	F383L	probably benign	Het
Fam193a	A	T	5: 34,597,879 (GRCm39)	T559S	probably damaging	Het
Galr2	T	C	11: 116,174,084 (GRCm39)	V238A	probably benign	Het
Gm3476	T	C	14: 6,118,411 (GRCm38)	I237M	probably benign	Het
Gm5160	A	T	18: 14,558,339 (GRCm39)	I139F	probably damaging	Het
Gpr15	T	C	16: 58,538,313 (GRCm39)	T259A	probably benign	Het
Iffo1	A	G	6: 125,126,746 (GRCm39)	K293E	possibly damaging	Het
Ikbip	T	A	10: 90,932,395 (GRCm39)	H346Q	probably benign	Het
Il4ra	G	A	7: 125,175,510 (GRCm39)	G573S	probably benign	Het
Ing2	A	T	8: 48,122,125 (GRCm39)	M141K	probably benign	Het
Itga6	T	C	2: 71,664,414 (GRCm39)	S517P	probably benign	Het
Itprid1	T	G	6: 55,945,330 (GRCm39)	S684A	probably damaging	Het
Kcnab1	A	G	3: 65,265,741 (GRCm39)	E295G	probably benign	Het
Klhl21	A	C	4: 152,099,835 (GRCm39)	Y515S	possibly damaging	Het
Lcn9	A	T	2: 25,714,553 (GRCm39)	Y139F	probably damaging	Het
Mcemp1	G	T	8: 3,717,052 (GRCm39)	L64F	probably null	Het
Mos	T	C	4: 3,870,814 (GRCm39)	D334G	possibly damaging	Het
Myo9b	T	G	8: 71,775,591 (GRCm39)	F338V	probably damaging	Het
Nefl	G	A	14: 68,323,979 (GRCm39)	V406M	probably damaging	Het
Nfam1	C	A	15: 82,885,689 (GRCm39)	R181L	probably damaging	Het
Ntn5	A	G	7: 45,335,925 (GRCm39)	R119G	probably damaging	Het
Or12e10	G	T	2: 87,640,938 (GRCm39)	C258F	probably damaging	Het
Or5b101	A	T	19: 13,005,095 (GRCm39)	Y199*	probably null	Het
Or7a40	T	C	16: 16,491,719 (GRCm39)	N42S	probably damaging	Het
Plch2	A	T	4: 155,073,960 (GRCm39)	V914E	probably damaging	Het
Ppp1r12c	T	C	7: 4,504,266 (GRCm39)	Q111R	probably null	Het
Ptchd3	T	A	11: 121,732,566 (GRCm39)	Y485*	probably null	Het
Ptchd4	T	A	17: 42,813,980 (GRCm39)	I627N	probably damaging	Het
Retnlb	T	C	16: 48,637,631 (GRCm39)	V19A	probably benign	Het
Rimbp2	T	A	5: 128,857,425 (GRCm39)	T809S	probably benign	Het
Slc22a16	C	T	10: 40,479,821 (GRCm39)	A631V	unknown	Het
Snai3	A	T	8: 123,183,073 (GRCm39)	H157Q	probably benign	Het
Snx15	T	C	19: 6,173,961 (GRCm39)	Y52C	probably damaging	Het
Strbp	T	C	2: 37,535,504 (GRCm39)	E68G	probably benign	Het
Sun1	T	A	5: 139,212,343 (GRCm39)	D155E	probably damaging	Het
Susd2	T	C	10: 75,474,183 (GRCm39)	D627G	probably benign	Het
Tas2r108	T	A	6: 40,470,614 (GRCm39)	I30K	probably damaging	Het
Tmc2	T	C	2: 130,090,571 (GRCm39)	V639A	probably damaging	Het
Trmt1	T	C	8: 85,424,299 (GRCm39)	Y445H	probably damaging	Het
Ttn	A	T	2: 76,597,554 (GRCm39)	N19786K	probably damaging	Het
Vmn1r79	T	G	7: 11,910,766 (GRCm39)	V216G	probably damaging	Het
Wdr64	C	A	1: 175,571,160 (GRCm39)	Y331*	probably null	Het
Zfyve28	A	T	5: 34,390,721 (GRCm39)	V180E	probably damaging	Het
Zic4	C	T	9: 91,261,447 (GRCm39)	T234I	possibly damaging	Het

Other mutations in Sema6c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01547:Sema6c	APN	3	95,079,709 (GRCm39)	missense	probably damaging	1.00
IGL01631:Sema6c	APN	3	95,077,714 (GRCm39)	missense	probably benign	0.10
IGL01799:Sema6c	APN	3	95,078,142 (GRCm39)	missense	probably damaging	1.00
IGL02237:Sema6c	APN	3	95,077,430 (GRCm39)	missense	probably damaging	1.00
IGL02852:Sema6c	APN	3	95,077,295 (GRCm39)	splice site	probably benign
IGL02874:Sema6c	APN	3	95,077,688 (GRCm39)	missense	probably damaging	1.00
IGL03003:Sema6c	APN	3	95,076,925 (GRCm39)	missense	probably damaging	1.00
BB005:Sema6c	UTSW	3	95,079,620 (GRCm39)	missense	probably damaging	1.00
BB015:Sema6c	UTSW	3	95,079,620 (GRCm39)	missense	probably damaging	1.00
R0558:Sema6c	UTSW	3	95,076,002 (GRCm39)	missense	probably damaging	1.00
R0582:Sema6c	UTSW	3	95,076,508 (GRCm39)	missense	probably damaging	1.00
R0590:Sema6c	UTSW	3	95,079,934 (GRCm39)	missense	probably damaging	1.00
R0685:Sema6c	UTSW	3	95,080,021 (GRCm39)	missense	possibly damaging	0.46
R1056:Sema6c	UTSW	3	95,078,527 (GRCm39)	missense	probably benign	0.15
R1721:Sema6c	UTSW	3	95,078,099 (GRCm39)	missense	probably damaging	0.98
R1867:Sema6c	UTSW	3	95,078,099 (GRCm39)	missense	probably damaging	0.98
R1868:Sema6c	UTSW	3	95,078,124 (GRCm39)	missense	probably damaging	0.99
R2016:Sema6c	UTSW	3	95,078,545 (GRCm39)	missense	probably benign	0.00
R2343:Sema6c	UTSW	3	95,074,394 (GRCm39)	missense	probably damaging	1.00
R2898:Sema6c	UTSW	3	95,080,129 (GRCm39)	missense	probably damaging	1.00
R4095:Sema6c	UTSW	3	95,080,505 (GRCm39)	missense	probably benign	0.03
R4999:Sema6c	UTSW	3	95,075,674 (GRCm39)	missense	probably damaging	1.00
R5263:Sema6c	UTSW	3	95,080,463 (GRCm39)	missense	probably benign	0.02
R6914:Sema6c	UTSW	3	95,080,519 (GRCm39)	missense	probably benign	0.00
R6942:Sema6c	UTSW	3	95,080,519 (GRCm39)	missense	probably benign	0.00
R7104:Sema6c	UTSW	3	95,076,156 (GRCm39)	missense	possibly damaging	0.95
R7524:Sema6c	UTSW	3	95,074,371 (GRCm39)	missense	probably benign	0.20
R7724:Sema6c	UTSW	3	95,080,510 (GRCm39)	missense	probably damaging	1.00
R7928:Sema6c	UTSW	3	95,079,620 (GRCm39)	missense	probably damaging	1.00
R8045:Sema6c	UTSW	3	95,080,535 (GRCm39)	missense	probably benign	0.27
R8243:Sema6c	UTSW	3	95,079,916 (GRCm39)	missense	probably damaging	1.00
R8790:Sema6c	UTSW	3	95,075,341 (GRCm39)	missense	probably benign	0.34
R9607:Sema6c	UTSW	3	95,076,545 (GRCm39)	missense	probably benign	0.03
R9653:Sema6c	UTSW	3	95,080,525 (GRCm39)	missense	probably benign	0.40
Z1177:Sema6c	UTSW	3	95,075,639 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CCAGCCATGTTTGAGAGCTTG -3'
(R):5'- ATGAAGCTTGAGCACTCCCAG -3'

Sequencing Primer
(F):5'- CCATGTTTGAGAGCTTGGAGGTG -3'
(R):5'- TTGAGCACTCCCAGGAGCAC -3'

Posted On

2019-06-07