Incidental Mutation 'R5245:Nsmf'
ID 401088
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 042816-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5245 (G1)
Quality Score 96
Status Validated
Chromosome 2
Chromosomal Location 24944370-24952893 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 24946119 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 202 (E202G)
Ref Sequence ENSEMBL: ENSMUSP00000141583 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006646] [ENSMUST00000045295] [ENSMUST00000074422] [ENSMUST00000100334] [ENSMUST00000102931] [ENSMUST00000114386] [ENSMUST00000114388] [ENSMUST00000116574] [ENSMUST00000132172] [ENSMUST00000140737] [ENSMUST00000137913] [ENSMUST00000144520] [ENSMUST00000152122] [ENSMUST00000155601]
AlphaFold Q99NF2
Predicted Effect probably damaging
Transcript: ENSMUST00000006646
AA Change: E202G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000006646
Gene: ENSMUSG00000006476
AA Change: E202G

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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 probably damaging
Transcript: ENSMUST00000074422
AA Change: E202G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000074022
Gene: ENSMUSG00000006476
AA Change: E202G

DomainStartEndE-ValueType
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 probably damaging
Transcript: ENSMUST00000100334
AA Change: E202G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000097908
Gene: ENSMUSG00000006476
AA Change: E202G

DomainStartEndE-ValueType
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 probably damaging
Transcript: ENSMUST00000102931
AA Change: E202G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000099995
Gene: ENSMUSG00000006476
AA Change: E202G

DomainStartEndE-ValueType
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 probably damaging
Transcript: ENSMUST00000114386
AA Change: E202G

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000110028
Gene: ENSMUSG00000006476
AA Change: E202G

DomainStartEndE-ValueType
low complexity region 3 28 N/A INTRINSIC
low complexity region 310 324 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000114388
AA Change: E202G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000110030
Gene: ENSMUSG00000006476
AA Change: E202G

DomainStartEndE-ValueType
low complexity region 3 28 N/A INTRINSIC
low complexity region 331 345 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000116574
AA Change: E202G

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000112273
Gene: ENSMUSG00000006476
AA Change: E202G

DomainStartEndE-ValueType
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: ENSMUST00000132082
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135328
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124309
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140733
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128517
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138536
Predicted Effect probably benign
Transcript: ENSMUST00000132172
SMART Domains Protein: ENSMUSP00000116106
Gene: ENSMUSG00000006476

DomainStartEndE-ValueType
low complexity region 3 28 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000140737
SMART Domains Protein: ENSMUSP00000141410
Gene: ENSMUSG00000006476

DomainStartEndE-ValueType
low complexity region 3 28 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000137913
SMART Domains Protein: ENSMUSP00000141577
Gene: ENSMUSG00000036833

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
low complexity region 3 12 N/A INTRINSIC
low complexity region 113 127 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141866
Predicted Effect probably damaging
Transcript: ENSMUST00000144520
AA Change: E202G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141583
Gene: ENSMUSG00000006476
AA Change: E202G

DomainStartEndE-ValueType
low complexity region 3 28 N/A INTRINSIC
low complexity region 283 294 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000175104
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155909
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152506
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141584
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184681
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154359
Predicted Effect probably benign
Transcript: ENSMUST00000152122
SMART Domains Protein: ENSMUSP00000121580
Gene: ENSMUSG00000006476

DomainStartEndE-ValueType
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
Predicted Effect probably benign
Transcript: ENSMUST00000155601
Meta Mutation Damage Score 0.1845 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.3%
Validation Efficiency 100% (51/51)
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: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd17b T A 19: 21,661,624 (GRCm39) Y270* probably null Het
Akap9 A T 5: 4,026,209 (GRCm39) Q59L probably damaging Het
Aloxe3 A T 11: 69,020,502 (GRCm39) Q182L probably benign Het
Arhgef5 G T 6: 43,242,614 (GRCm39) probably benign Het
Bcas3 T A 11: 85,449,912 (GRCm39) N663K probably damaging Het
Cimap3 T C 3: 105,921,770 (GRCm39) H51R possibly damaging Het
Cntfr A T 4: 41,670,879 (GRCm39) W95R possibly damaging Het
Dcun1d4 A G 5: 73,714,657 (GRCm39) T275A probably benign Het
Eps8l1 A G 7: 4,473,873 (GRCm39) R227G probably damaging Het
Ets2 G A 16: 95,513,304 (GRCm39) W160* probably null Het
Flt4 AC ACC 11: 49,541,861 (GRCm39) probably null Het
Fsip2 A G 2: 82,823,505 (GRCm39) M6413V probably benign Het
Gm14401 C T 2: 176,778,471 (GRCm39) P186S probably damaging Het
Hrc G A 7: 44,984,855 (GRCm39) G2D probably damaging Het
Kcnq3 A G 15: 65,903,284 (GRCm39) V142A possibly damaging Het
Lama3 G A 18: 12,552,950 (GRCm39) C454Y probably damaging Het
Lrrk2 A G 15: 91,680,292 (GRCm39) T2068A probably damaging Het
Mab21l2 T C 3: 86,454,799 (GRCm39) E67G possibly damaging Het
Map3k5 G A 10: 20,016,437 (GRCm39) V1343I probably benign Het
Mcm4 T A 16: 15,448,289 (GRCm39) T423S probably benign Het
Mmp16 A G 4: 18,054,596 (GRCm39) probably benign Het
Nat3 C T 8: 68,000,832 (GRCm39) T237I probably benign Het
Nol4 A T 18: 22,828,179 (GRCm39) *484R probably null Het
Olfml2b T C 1: 170,496,443 (GRCm39) V358A probably benign Het
Or2v2 T A 11: 49,004,116 (GRCm39) I146F probably benign Het
Or4b1d T A 2: 89,968,606 (GRCm39) K292N probably damaging Het
Osbpl1a T C 18: 12,891,910 (GRCm39) E466G probably damaging Het
Pim3 A G 15: 88,747,404 (GRCm39) E90G possibly damaging Het
Recql5 T C 11: 115,784,385 (GRCm39) E905G probably damaging Het
Rnf31 T G 14: 55,839,163 (GRCm39) L925R probably damaging Het
Secisbp2l A G 2: 125,589,511 (GRCm39) V679A probably damaging Het
Setdb2 T A 14: 59,663,943 (GRCm39) E68V probably null Het
Shtn1 T A 19: 59,020,652 (GRCm39) N190I possibly damaging Het
Slc25a25 G A 2: 32,311,340 (GRCm39) Q14* probably null Het
Snrnp27 A G 6: 86,659,941 (GRCm39) S18P unknown Het
Srsf11 C T 3: 157,728,981 (GRCm39) probably benign Het
Tbx5 T C 5: 120,021,230 (GRCm39) V412A possibly damaging Het
Tcea3 A G 4: 135,991,813 (GRCm39) T166A probably benign Het
Tdrp A T 8: 14,024,479 (GRCm39) probably benign Het
Tent5a G T 9: 85,208,401 (GRCm39) Q160K possibly damaging Het
Tmem132e T C 11: 82,333,464 (GRCm39) V624A probably damaging Het
Tnnt1 T C 7: 4,513,066 (GRCm39) D72G probably damaging Het
Trim80 C A 11: 115,332,398 (GRCm39) H197N probably damaging Het
Zfp322a A T 13: 23,541,156 (GRCm39) C195* probably null Het
Zfp335 A G 2: 164,736,678 (GRCm39) S986P probably benign Het
Other mutations in Nsmf
AlleleSourceChrCoordTypePredicted EffectPPH 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
R5687:Nsmf UTSW 2 24,946,079 (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'- AGCCATTGAGCTAGCAGTGG -3'
(R):5'- TTCACAGGATTTGGGCGAGG -3'

Sequencing Primer
(F):5'- CCATTGAGCTAGCAGTGGTAAAAG -3'
(R):5'- CGAGGAGGTGAGCTCAGATG -3'
Posted On 2016-07-06