Mutagenetix > Incidental Mutation

Incidental Mutation 'R7898:Spag4'

609800

Institutional Source

Beutler Lab

Gene Symbol

Spag4

Ensembl Gene

ENSMUSG00000038180

Gene Name

sperm associated antigen 4

Synonyms

Sun4, 1700041K21Rik

MMRRC Submission

045950-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7898 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

155907108-155911421 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 155911244 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 393 (D393V)

Ref Sequence

ENSEMBL: ENSMUSP00000036484 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038860] [ENSMUST00000079312] [ENSMUST00000109607] [ENSMUST00000109608] [ENSMUST00000132494] [ENSMUST00000136296] [ENSMUST00000137966] [ENSMUST00000138178] [ENSMUST00000147627] [ENSMUST00000184265]

AlphaFold

Q9JJF2

Predicted Effect

probably damaging
Transcript: ENSMUST00000038860
AA Change: D393V

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000036484
Gene: ENSMUSG00000038180
AA Change: D393V

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	19	37	N/A	INTRINSIC
transmembrane domain	137	159	N/A	INTRINSIC
transmembrane domain	166	188	N/A	INTRINSIC
low complexity region	214	222	N/A	INTRINSIC
Pfam:Sad1_UNC	293	426	1.9e-44	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000079312

SMART Domains

Protein: ENSMUSP00000078292
Gene: ENSMUSG00000074643

Domain	Start	End	E-Value	Type
C2	6	112	3.64e-9	SMART
C2	137	242	8.76e-12	SMART
VWA	282	468	8.96e-2	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000109607

SMART Domains

Protein: ENSMUSP00000105236
Gene: ENSMUSG00000074643

Domain	Start	End	E-Value	Type
C2	6	112	3.64e-9	SMART
C2	137	242	8.76e-12	SMART
VWA	282	484	9.5e-15	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000109608

SMART Domains

Protein: ENSMUSP00000105237
Gene: ENSMUSG00000074643

Domain	Start	End	E-Value	Type
C2	6	112	3.64e-9	SMART
C2	137	242	8.76e-12	SMART
VWA	282	484	9.5e-15	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000127956

SMART Domains

Protein: ENSMUSP00000114923
Gene: ENSMUSG00000098950

Domain	Start	End	E-Value	Type
low complexity region	10	28	N/A	INTRINSIC
low complexity region	73	172	N/A	INTRINSIC
RRM	217	287	1.05e-1	SMART
RRM	343	415	2.73e-7	SMART
RRM	457	529	8.73e-6	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000131144

Predicted Effect

probably benign
Transcript: ENSMUST00000132494

SMART Domains

Protein: ENSMUSP00000139175
Gene: ENSMUSG00000098950

Domain	Start	End	E-Value	Type
Pfam:RRM_6	5	70	1.5e-5	PFAM
low complexity region	98	116	N/A	INTRINSIC
low complexity region	161	260	N/A	INTRINSIC
RRM	305	375	1.05e-1	SMART
RRM	431	503	2.73e-7	SMART
RRM	545	617	8.73e-6	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000136296

SMART Domains

Protein: ENSMUSP00000122994
Gene: ENSMUSG00000074643

Domain	Start	End	E-Value	Type
C2	6	112	3.64e-9	SMART
C2	123	218	7.88e-5	SMART
Pfam:Copine	279	378	2.3e-41	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000137966

SMART Domains

Protein: ENSMUSP00000118715
Gene: ENSMUSG00000038180

Domain	Start	End	E-Value	Type
transmembrane domain	43	65	N/A	INTRINSIC
transmembrane domain	72	94	N/A	INTRINSIC
coiled coil region	112	147	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000138178

Predicted Effect

probably benign
Transcript: ENSMUST00000140109

SMART Domains

Protein: ENSMUSP00000121998
Gene: ENSMUSG00000074643

Domain	Start	End	E-Value	Type
Pfam:Copine	1	148	2.1e-50	PFAM
Pfam:vWA-TerF-like	5	111	2.5e-7	PFAM
low complexity region	167	185	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000147627

SMART Domains

Protein: ENSMUSP00000116982
Gene: ENSMUSG00000074643

Domain	Start	End	E-Value	Type
C2	6	112	3.64e-9	SMART
C2	137	242	8.76e-12	SMART
Pfam:Copine	303	350	1.3e-16	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000183733

Predicted Effect

probably benign
Transcript: ENSMUST00000184265

SMART Domains

Protein: ENSMUSP00000138888
Gene: ENSMUSG00000074643

Domain	Start	End	E-Value	Type
C2	6	112	3.64e-9	SMART

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

99% (69/70)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The mammalian sperm flagellum contains two cytoskeletal structures associated with the axoneme: the outer dense fibers surrounding the axoneme in the midpiece and principal piece and the fibrous sheath surrounding the outer dense fibers in the principal piece of the tail. Defects in these structures are associated with abnormal tail morphology, reduced sperm motility, and infertility. In the rat, the protein encoded by this gene associates with an outer dense fiber protein via a leucine zipper motif and localizes to the microtubules of the manchette and axoneme during sperm tail development. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
PHENOTYPE: Mice homozygous for a knock-out allele show disrupted spermiogenesis, severe defects in sperm head formation, abnormal manchette morphology, globozoospermia, and male infertility. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acaca	T	C	11: 84,255,275 (GRCm39)		probably null	Het
Afg2a	T	G	3: 37,474,620 (GRCm39)	M44R	probably benign	Het
Ankef1	C	A	2: 136,395,618 (GRCm39)	N649K	probably benign	Het
Arl5b	T	A	2: 15,079,869 (GRCm39)	S147T	probably damaging	Het
Arnt2	A	T	7: 83,918,155 (GRCm39)		probably null	Het
Ash1l	A	G	3: 88,890,932 (GRCm39)	E937G	possibly damaging	Het
Asxl1	T	G	2: 153,241,854 (GRCm39)	S802R	possibly damaging	Het
Cacna1h	T	A	17: 25,611,250 (GRCm39)	H516L	probably damaging	Het
Cad	A	G	5: 31,218,829 (GRCm39)	Y550C	probably damaging	Het
Cdo1	A	G	18: 46,861,157 (GRCm39)	I18T	probably benign	Het
Cfap251	A	T	5: 123,460,517 (GRCm39)	I1160F	probably damaging	Het
Chd2	A	G	7: 73,169,223 (GRCm39)		probably null	Het
Dbf4	A	G	5: 8,458,232 (GRCm39)		probably null	Het
Dcdc2a	A	T	13: 25,286,361 (GRCm39)	R132W	possibly damaging	Het
Dnah10	T	C	5: 124,859,425 (GRCm39)	S2131P	probably damaging	Het
Eef2k	A	G	7: 120,494,441 (GRCm39)	Y599C	probably damaging	Het
Eno2	C	T	6: 124,744,225 (GRCm39)		probably null	Het
Fam124b	T	A	1: 80,191,512 (GRCm39)		probably benign	Het
Fezf2	A	G	14: 12,342,701 (GRCm38)	I388T	possibly damaging	Het
Gbp11	T	C	5: 105,472,798 (GRCm39)	N542S	probably benign	Het
Gdpd1	T	A	11: 86,932,639 (GRCm39)	I229F	probably damaging	Het
Gria1	T	A	11: 57,133,591 (GRCm39)	V490E	probably damaging	Het
Grm8	G	A	6: 27,762,422 (GRCm39)	R268C	probably damaging	Het
Hectd4	T	A	5: 121,469,880 (GRCm39)	S2592T	probably benign	Het
Herpud1	C	T	8: 95,118,828 (GRCm39)	T194I	probably benign	Het
Hspa1b	T	C	17: 35,177,167 (GRCm39)	T273A	probably benign	Het
Iftap	T	A	2: 101,416,747 (GRCm39)	K67N	probably benign	Het
Ighm	T	A	12: 113,384,873 (GRCm39)	K327*	probably null	Het
Igkv3-4	A	T	6: 70,649,297 (GRCm39)	I99F	probably damaging	Het
Iqca1l	T	C	5: 24,758,643 (GRCm39)	E117G	probably damaging	Het
Isl2	C	A	9: 55,449,723 (GRCm39)	S97R	probably benign	Het
Klhl12	A	T	1: 134,386,219 (GRCm39)	I4F	probably benign	Het
Lgalsl2	G	A	7: 5,362,441 (GRCm39)	R24H	probably benign	Het
Lrp2	T	C	2: 69,271,710 (GRCm39)	E4074G	probably benign	Het
Mcm3ap	A	G	10: 76,342,441 (GRCm39)	N1645D	probably damaging	Het
Mettl23	T	C	11: 116,736,679 (GRCm39)		probably benign	Het
Mettl24	A	G	10: 40,686,478 (GRCm39)	E285G	probably benign	Het
Mis18bp1	A	G	12: 65,196,246 (GRCm39)	L506P	probably benign	Het
Mup18	G	T	4: 61,590,925 (GRCm39)		probably null	Het
Myom1	T	C	17: 71,352,747 (GRCm39)	L357P	probably benign	Het
Nkx2-9	G	A	12: 56,659,031 (GRCm39)	A61V	probably benign	Het
Or52n5	C	T	7: 104,588,573 (GRCm39)	A280V	probably damaging	Het
Pbx1	A	T	1: 168,012,616 (GRCm39)	M340K	probably benign	Het
Pcdhb17	A	T	18: 37,618,233 (GRCm39)	N8Y	probably benign	Het
Pex13	C	A	11: 23,600,929 (GRCm39)		probably null	Het
Pierce1	TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC	TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC	2: 28,356,122 (GRCm39)		probably benign	Het
Plxnb1	A	G	9: 108,943,408 (GRCm39)	R1884G	probably damaging	Het
Polq	T	A	16: 36,865,245 (GRCm39)	V699E	probably damaging	Het
Ppl	C	T	16: 4,906,725 (GRCm39)	R1190H	probably damaging	Het
Prr14l	A	T	5: 32,987,310 (GRCm39)	H728Q	probably benign	Het
Prss12	T	C	3: 123,300,145 (GRCm39)	V752A	possibly damaging	Het
Prss56	A	G	1: 87,111,921 (GRCm39)	S51G	probably benign	Het
Pwp2	G	A	10: 78,009,240 (GRCm39)	R854W	probably damaging	Het
Rhobtb2	C	T	14: 70,033,746 (GRCm39)	C493Y	probably damaging	Het
Rictor	C	T	15: 6,801,635 (GRCm39)	S441L	probably benign	Het
Rusf1	C	A	7: 127,897,177 (GRCm39)	A27S	probably benign	Het
Scap	A	G	9: 110,213,811 (GRCm39)	N1258S	possibly damaging	Het
Sec31a	C	T	5: 100,547,336 (GRCm39)	G218R	probably damaging	Het
Siglec15	A	T	18: 78,086,914 (GRCm39)	M315K	probably benign	Het
Slc17a6	G	A	7: 51,308,573 (GRCm39)		probably null	Het
Smchd1	T	C	17: 71,684,813 (GRCm39)		probably null	Het
Sulf1	A	G	1: 12,875,518 (GRCm39)	N176S	probably damaging	Het
Tmem9	T	A	1: 135,955,125 (GRCm39)		probably null	Het
Tnpo3	T	C	6: 29,565,223 (GRCm39)	I577V	probably benign	Het
Tti1	A	C	2: 157,835,390 (GRCm39)	I956S	probably benign	Het
Wdr81	T	C	11: 75,344,725 (GRCm39)	R181G	probably benign	Het
Zfp462	T	A	4: 55,012,995 (GRCm39)	C1654S	probably damaging	Het
Zfp74	A	T	7: 29,635,380 (GRCm39)	C109*	probably null	Het
Znrf4	A	G	17: 56,818,681 (GRCm39)	C209R	probably damaging	Het
Zzef1	T	G	11: 72,687,373 (GRCm39)	L84R	probably damaging	Het

Other mutations in Spag4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01409:Spag4	APN	2	155,911,252 (GRCm39)	missense	possibly damaging	0.88
IGL01843:Spag4	APN	2	155,910,417 (GRCm39)	missense	probably benign	0.04
IGL02200:Spag4	APN	2	155,908,517 (GRCm39)	missense	probably benign	0.14
IGL02506:Spag4	APN	2	155,911,142 (GRCm39)	missense	probably damaging	1.00
IGL02570:Spag4	APN	2	155,910,364 (GRCm39)	missense	possibly damaging	0.60
IGL03302:Spag4	APN	2	155,910,340 (GRCm39)	missense	probably damaging	0.97
R0127:Spag4	UTSW	2	155,909,962 (GRCm39)	missense	probably damaging	0.99
R0314:Spag4	UTSW	2	155,909,229 (GRCm39)	unclassified	probably benign
R0441:Spag4	UTSW	2	155,909,899 (GRCm39)	missense	probably damaging	1.00
R1699:Spag4	UTSW	2	155,907,342 (GRCm39)	missense	probably damaging	1.00
R5270:Spag4	UTSW	2	155,907,853 (GRCm39)	intron	probably benign
R5293:Spag4	UTSW	2	155,908,111 (GRCm39)	missense	probably benign	0.07
R6092:Spag4	UTSW	2	155,907,696 (GRCm39)	intron	probably benign
R7138:Spag4	UTSW	2	155,908,519 (GRCm39)	missense	probably benign	0.00
R7300:Spag4	UTSW	2	155,907,541 (GRCm39)	missense	probably benign	0.06
R8756:Spag4	UTSW	2	155,908,493 (GRCm39)	missense	possibly damaging	0.94
R9025:Spag4	UTSW	2	155,910,424 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- ACGAGACTGAAGTGTTCTTGG -3'
(R):5'- TGCTATACCACAGGCAGCAG -3'

Sequencing Primer
(F):5'- AAGTGTTCTTGGGGAAATTCATC -3'
(R):5'- ACGCACTTTTCTTTAGCACAAAC -3'

Posted On

2019-12-20