Mutagenetix > Incidental Mutation

Incidental Mutation 'R5687:Nsmf'

443402

Institutional Source

Beutler Lab

Gene Symbol

Nsmf

Ensembl Gene

ENSMUSG00000006476

Gene Name

NMDA receptor synaptonuclear signaling and neuronal migration factor

Synonyms

Nelf, Jacob

MMRRC Submission

043320-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5687 (G1)

Quality Score

169

Status

Validated

Chromosome

Chromosomal Location

24944370-24952893 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 24946079 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 189 (P189S)

Ref Sequence

ENSEMBL: ENSMUSP00000110030 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006646] [ENSMUST00000045295] [ENSMUST00000074422] [ENSMUST00000100334] [ENSMUST00000102931] [ENSMUST00000114386] [ENSMUST00000114388] [ENSMUST00000116574] [ENSMUST00000144520] [ENSMUST00000140737] [ENSMUST00000137913] [ENSMUST00000132172] [ENSMUST00000155601] [ENSMUST00000152122]

AlphaFold

Q99NF2

Predicted Effect

possibly damaging
Transcript: ENSMUST00000006646
AA Change: P189S

PolyPhen 2 Score 0.886 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000006646
Gene: ENSMUSG00000006476
AA Change: P189S

Domain	Start	End	E-Value	Type
low complexity region	3	28	N/A	INTRINSIC
low complexity region	281	292	N/A	INTRINSIC
low complexity region	361	375	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000045295

SMART Domains

Protein: ENSMUSP00000044078
Gene: ENSMUSG00000036833

Domain	Start	End	E-Value	Type
transmembrane domain	36	58	N/A	INTRINSIC
low complexity region	59	66	N/A	INTRINSIC
cNMP	170	295	2.06e-12	SMART
low complexity region	439	444	N/A	INTRINSIC
cNMP	481	600	1.16e-6	SMART
cNMP	603	716	1.55e-7	SMART
Pfam:Patatin	950	1116	3.2e-24	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000074422
AA Change: P189S

PolyPhen 2 Score 0.886 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000074022
Gene: ENSMUSG00000006476
AA Change: P189S

Domain	Start	End	E-Value	Type
low complexity region	3	28	N/A	INTRINSIC
low complexity region	258	269	N/A	INTRINSIC
low complexity region	338	352	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000100334
AA Change: P189S

PolyPhen 2 Score 0.886 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000097908
Gene: ENSMUSG00000006476
AA Change: P189S

Domain	Start	End	E-Value	Type
low complexity region	3	28	N/A	INTRINSIC
low complexity region	283	294	N/A	INTRINSIC
low complexity region	363	377	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000102931
AA Change: P189S

PolyPhen 2 Score 0.886 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000099995
Gene: ENSMUSG00000006476
AA Change: P189S

Domain	Start	End	E-Value	Type
low complexity region	3	28	N/A	INTRINSIC
low complexity region	260	271	N/A	INTRINSIC
low complexity region	340	354	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000114386
AA Change: P189S

PolyPhen 2 Score 0.934 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000110028
Gene: ENSMUSG00000006476
AA Change: P189S

Domain	Start	End	E-Value	Type
low complexity region	3	28	N/A	INTRINSIC
low complexity region	310	324	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000114388
AA Change: P189S

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000110030
Gene: ENSMUSG00000006476
AA Change: P189S

Domain	Start	End	E-Value	Type
low complexity region	3	28	N/A	INTRINSIC
low complexity region	331	345	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135328

Predicted Effect

possibly damaging
Transcript: ENSMUST00000116574
AA Change: P189S

PolyPhen 2 Score 0.886 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000112273
Gene: ENSMUSG00000006476
AA Change: P189S

Domain	Start	End	E-Value	Type
low complexity region	3	28	N/A	INTRINSIC
low complexity region	260	271	N/A	INTRINSIC
low complexity region	340	354	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141866

Predicted Effect

probably benign
Transcript: ENSMUST00000144520
AA Change: P189S

PolyPhen 2 Score 0.289 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000141583
Gene: ENSMUSG00000006476
AA Change: P189S

Domain	Start	End	E-Value	Type
low complexity region	3	28	N/A	INTRINSIC
low complexity region	283	294	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128517

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140733

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138536

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124309

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132082

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141584

Predicted Effect

probably benign
Transcript: ENSMUST00000140737

SMART Domains

Protein: ENSMUSP00000141410
Gene: ENSMUSG00000006476

Domain	Start	End	E-Value	Type
low complexity region	3	28	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000137913

SMART Domains

Protein: ENSMUSP00000141577
Gene: ENSMUSG00000036833

Domain	Start	End	E-Value	Type
transmembrane domain	10	32	N/A	INTRINSIC
low complexity region	33	40	N/A	INTRINSIC
Pfam:cNMP_binding	162	200	2.7e-5	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000134744

SMART Domains

Protein: ENSMUSP00000120376
Gene: ENSMUSG00000006476

Domain	Start	End	E-Value	Type
low complexity region	3	12	N/A	INTRINSIC
low complexity region	113	127	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000132172

SMART Domains

Protein: ENSMUSP00000116106
Gene: ENSMUSG00000006476

Domain	Start	End	E-Value	Type
low complexity region	3	28	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152506

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184681

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155909

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175104

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154359

Predicted Effect

probably benign
Transcript: ENSMUST00000155601

Predicted Effect

probably benign
Transcript: ENSMUST00000152122

SMART Domains

Protein: ENSMUSP00000121580
Gene: ENSMUSG00000006476

Domain	Start	End	E-Value	Type
low complexity region	3	28	N/A	INTRINSIC
Pfam:IQ	62	80	2.5e-4	PFAM
low complexity region	114	125	N/A	INTRINSIC
low complexity region	194	208	N/A	INTRINSIC

Meta Mutation Damage Score

0.1139

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.4%
20x: 95.6%

Validation Efficiency

99% (72/73)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is involved in guidance of olfactory axon projections and migration of luteinizing hormone-releasing hormone neurons. Defects in this gene are a cause of idiopathic hypogonadotropic hypogonadism (IHH). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit delayed sexual maturation in female mice with decreased uterus and ovary weights, reduced male and female fertility, and reduced gonadotrophs in female mice. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts20	T	A	15: 94,223,852 (GRCm39)	D1292V	probably benign	Het
Adcy2	A	T	13: 68,768,938 (GRCm39)	C1063*	probably null	Het
Adcy2	A	T	13: 68,790,688 (GRCm39)	V892D	probably damaging	Het
Agtpbp1	T	C	13: 59,648,329 (GRCm39)	D497G	probably benign	Het
Anks1b	A	C	10: 90,750,573 (GRCm39)	I195L	probably benign	Het
Asmt	G	T	X: 169,111,749 (GRCm39)	S377I	unknown	Het
C1s1	T	A	6: 124,517,909 (GRCm39)	T24S	probably benign	Het
Ccdc85a	A	T	11: 28,342,854 (GRCm39)		probably benign	Het
Ccndbp1	T	C	2: 120,845,183 (GRCm39)		probably benign	Het
Cct8	T	C	16: 87,285,709 (GRCm39)	I250V	probably benign	Het
Cmya5	T	C	13: 93,234,684 (GRCm39)	T135A	possibly damaging	Het
Col11a1	T	C	3: 114,010,752 (GRCm39)		probably benign	Het
Crybg3	A	G	16: 59,379,529 (GRCm39)	M575T	probably benign	Het
Dmp1	C	T	5: 104,354,952 (GRCm39)		probably benign	Het
Emc1	G	T	4: 139,102,691 (GRCm39)	R950L	probably damaging	Het
Enpep	T	C	3: 129,092,743 (GRCm39)		probably null	Het
Eya1	G	A	1: 14,253,476 (GRCm39)	T500I	probably damaging	Het
Fam169a	T	C	13: 97,230,126 (GRCm39)	F54L	probably damaging	Het
Fbxo8	A	G	8: 57,044,552 (GRCm39)	K285R	probably damaging	Het
Galnt1	A	T	18: 24,405,807 (GRCm39)	E416D	probably benign	Het
Gcc1	T	A	6: 28,419,232 (GRCm39)		probably null	Het
Gm10800	T	A	2: 98,496,965 (GRCm39)	Y196F	probably benign	Het
Gmpr	T	A	13: 45,692,496 (GRCm39)		probably null	Het
Jrkl	C	T	9: 13,244,387 (GRCm39)	E425K	probably benign	Het
Kl	T	G	5: 150,911,931 (GRCm39)	I560S	possibly damaging	Het
Kyat3	C	A	3: 142,440,343 (GRCm39)	R356S	probably null	Het
Lrig2	C	T	3: 104,371,388 (GRCm39)		probably null	Het
Lrrc47	A	G	4: 154,100,140 (GRCm39)	T239A	probably benign	Het
Map4k2	T	C	19: 6,395,672 (GRCm39)		probably benign	Het
Mon2	A	G	10: 122,844,144 (GRCm39)	S1469P	probably damaging	Het
Mthfd1l	G	A	10: 3,940,002 (GRCm39)		probably null	Het
Mvk	G	T	5: 114,588,826 (GRCm39)	G144V	probably damaging	Het
Nasp	T	A	4: 116,463,002 (GRCm39)		probably benign	Het
Ndst4	A	C	3: 125,232,258 (GRCm39)	N276H	possibly damaging	Het
Nt5m	T	G	11: 59,743,649 (GRCm39)	D92E	probably benign	Het
Or10g6	T	G	9: 39,933,731 (GRCm39)	L14R	probably damaging	Het
Or4k39	T	C	2: 111,239,033 (GRCm39)		noncoding transcript	Het
Or4p23	A	T	2: 88,577,094 (GRCm39)	I46N	probably damaging	Het
Pan3	T	A	5: 147,391,982 (GRCm39)	I119N	probably damaging	Het
Pard6b	A	T	2: 167,940,546 (GRCm39)	S178C	probably damaging	Het
Parl	A	G	16: 20,106,728 (GRCm39)		probably benign	Het
Pdk2	A	G	11: 94,919,851 (GRCm39)		probably benign	Het
Prag1	A	G	8: 36,613,967 (GRCm39)	E1173G	probably benign	Het
Prph2	T	A	17: 47,234,391 (GRCm39)	L320Q	probably damaging	Het
Psmd3	T	C	11: 98,584,495 (GRCm39)	I200T	probably damaging	Het
Rhbdd3	T	A	11: 5,055,707 (GRCm39)	S324T	probably damaging	Het
Rps6-ps2	A	T	8: 89,533,112 (GRCm39)		noncoding transcript	Het
Rps8	G	C	4: 117,012,352 (GRCm39)		probably benign	Het
Samd4	A	G	14: 47,254,022 (GRCm39)	N61S	probably benign	Het
Sfrp2	G	A	3: 83,674,146 (GRCm39)	A100T	probably damaging	Het
Sh3bp5	C	A	14: 31,099,452 (GRCm39)	R265L	probably benign	Het
Slc6a13	A	G	6: 121,279,700 (GRCm39)	T25A	probably benign	Het
Sntg1	C	A	1: 8,533,667 (GRCm39)	R329L	possibly damaging	Het
Sorbs2	T	C	8: 46,228,669 (GRCm39)	F285L	probably damaging	Het
Speg	T	C	1: 75,395,773 (GRCm39)		probably null	Het
Srgap1	T	C	10: 121,661,541 (GRCm39)	Y533C	probably damaging	Het
Supt5	C	A	7: 28,017,188 (GRCm39)	S668I	probably benign	Het
Taf6l	T	G	19: 8,750,676 (GRCm39)	I133L	probably benign	Het
Thrap3	G	A	4: 126,074,279 (GRCm39)		probably benign	Het
Tmem115	A	G	9: 107,412,054 (GRCm39)	N126S	probably benign	Het
Trgc1	A	T	13: 19,400,729 (GRCm39)	I153F	unknown	Het
Tspoap1	T	A	11: 87,667,952 (GRCm39)	I1192N	probably damaging	Het
Vcan	T	C	13: 89,826,253 (GRCm39)	I3184V	probably damaging	Het
Yeats4	G	A	10: 117,051,585 (GRCm39)	T224M	probably benign	Het
Zc3h13	A	T	14: 75,569,400 (GRCm39)	R1416*	probably null	Het
Zmynd12	T	A	4: 119,299,098 (GRCm39)	Y193N	probably damaging	Het

Other mutations in Nsmf

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02877:Nsmf	APN	2	24,945,968 (GRCm39)	missense	possibly damaging	0.47
IGL02965:Nsmf	APN	2	24,951,774 (GRCm39)	missense	probably damaging	0.99
R0079:Nsmf	UTSW	2	24,949,096 (GRCm39)	splice site	probably benign
R0786:Nsmf	UTSW	2	24,950,522 (GRCm39)	missense	probably damaging	1.00
R1553:Nsmf	UTSW	2	24,950,271 (GRCm39)	missense	probably damaging	1.00
R4091:Nsmf	UTSW	2	24,950,871 (GRCm39)	missense	probably damaging	1.00
R4750:Nsmf	UTSW	2	24,945,038 (GRCm39)	missense	probably damaging	1.00
R5032:Nsmf	UTSW	2	24,945,073 (GRCm39)	critical splice donor site	probably null
R5091:Nsmf	UTSW	2	24,950,464 (GRCm39)	intron	probably benign
R5245:Nsmf	UTSW	2	24,946,119 (GRCm39)	missense	probably damaging	1.00
R6323:Nsmf	UTSW	2	24,945,063 (GRCm39)	missense	possibly damaging	0.93
R9063:Nsmf	UTSW	2	24,952,622 (GRCm39)	missense	probably benign	0.03
R9710:Nsmf	UTSW	2	24,949,077 (GRCm39)	missense	probably null	0.00

Predicted Primers

PCR Primer
(F):5'- AGCCATTGAGCTAGCAGTG -3'
(R):5'- TTCACAGGATTTGGGCGAGG -3'

Sequencing Primer
(F):5'- CCATTGAGCTAGCAGTGGTAAAAG -3'
(R):5'- CGAGGAGGTGAGCTCAGATG -3'

Posted On

2016-11-09