Incidental Mutation 'R6554:Lrfn4'
| ID |
521878 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lrfn4
|
| Ensembl Gene |
ENSMUSG00000045045 |
| Gene Name |
leucine rich repeat and fibronectin type III domain containing 4 |
| Synonyms |
SALM3 |
| MMRRC Submission |
044679-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.433)
|
| Stock # |
R6554 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
4661813-4665695 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 4663914 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 207
(T207A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000109453
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000053597]
[ENSMUST00000068004]
[ENSMUST00000113822]
[ENSMUST00000113825]
[ENSMUST00000224726]
|
| AlphaFold |
Q80XU8 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000053597
AA Change: T207A
PolyPhen 2
Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000050039
Gene: ENSMUSG00000045045
AA Change: T207A
| Domain | Start | End | E-Value | Type |
|---|
|
LRRNT
|
16 |
52 |
1.16e0 |
SMART |
|
LRR
|
71 |
94 |
3.86e0 |
SMART |
|
LRR_TYP
|
95 |
118 |
9.44e-2 |
SMART |
|
LRR
|
120 |
142 |
1.23e0 |
SMART |
|
LRR
|
144 |
166 |
1.09e1 |
SMART |
|
LRR_TYP
|
168 |
191 |
7.37e-4 |
SMART |
|
LRR
|
192 |
215 |
1.45e1 |
SMART |
|
LRRCT
|
234 |
279 |
1.27e-3 |
SMART |
|
IGc2
|
293 |
358 |
3.35e-14 |
SMART |
|
FN3
|
403 |
484 |
1.77e-2 |
SMART |
|
transmembrane domain
|
517 |
539 |
N/A |
INTRINSIC |
|
low complexity region
|
565 |
585 |
N/A |
INTRINSIC |
|
low complexity region
|
614 |
626 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000068004
|
| SMART Domains |
Protein: ENSMUSP00000063825
Gene: ENSMUSG00000024892
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
8 |
22 |
N/A |
INTRINSIC |
|
Pfam:CPSase_L_chain
|
37 |
147 |
3.3e-45 |
PFAM |
|
Pfam:ATP-grasp_4
|
149 |
334 |
3.9e-19 |
PFAM |
|
Pfam:CPSase_L_D2
|
152 |
361 |
7.2e-77 |
PFAM |
|
Pfam:Dala_Dala_lig_C
|
161 |
329 |
1.5e-11 |
PFAM |
|
Biotin_carb_C
|
376 |
483 |
1.21e-50 |
SMART |
|
low complexity region
|
513 |
541 |
N/A |
INTRINSIC |
|
Pfam:HMGL-like
|
564 |
838 |
8.2e-29 |
PFAM |
|
Pfam:PYC_OADA
|
862 |
1062 |
1.4e-72 |
PFAM |
|
Pfam:Biotin_lipoyl
|
1111 |
1178 |
1.4e-20 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000113822
AA Change: T207A
PolyPhen 2
Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000109453
Gene: ENSMUSG00000045045
AA Change: T207A
| Domain | Start | End | E-Value | Type |
|---|
|
LRRNT
|
16 |
52 |
1.16e0 |
SMART |
|
LRR
|
71 |
94 |
3.86e0 |
SMART |
|
LRR_TYP
|
95 |
118 |
9.44e-2 |
SMART |
|
LRR
|
120 |
142 |
1.23e0 |
SMART |
|
LRR
|
144 |
166 |
1.09e1 |
SMART |
|
LRR_TYP
|
168 |
191 |
7.37e-4 |
SMART |
|
LRR
|
192 |
215 |
1.45e1 |
SMART |
|
LRRCT
|
234 |
279 |
1.27e-3 |
SMART |
|
IGc2
|
293 |
358 |
3.35e-14 |
SMART |
|
FN3
|
403 |
484 |
1.77e-2 |
SMART |
|
transmembrane domain
|
517 |
539 |
N/A |
INTRINSIC |
|
low complexity region
|
565 |
585 |
N/A |
INTRINSIC |
|
low complexity region
|
614 |
626 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000113825
|
| SMART Domains |
Protein: ENSMUSP00000109456
Gene: ENSMUSG00000024892
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
7 |
21 |
N/A |
INTRINSIC |
|
Pfam:CPSase_L_chain
|
36 |
146 |
1.1e-43 |
PFAM |
|
Pfam:ATP-grasp_4
|
148 |
332 |
2.9e-19 |
PFAM |
|
Pfam:CPSase_L_D2
|
151 |
360 |
4.2e-77 |
PFAM |
|
Pfam:Dala_Dala_lig_C
|
158 |
328 |
7.9e-13 |
PFAM |
|
Biotin_carb_C
|
375 |
482 |
1.21e-50 |
SMART |
|
low complexity region
|
512 |
540 |
N/A |
INTRINSIC |
|
Pfam:HMGL-like
|
571 |
821 |
3.4e-28 |
PFAM |
|
Pfam:PYC_OADA
|
861 |
1062 |
3.4e-69 |
PFAM |
|
Pfam:Biotin_lipoyl
|
1110 |
1177 |
1.8e-21 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000224726
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.4%
- 20x: 98.0%
|
| Validation Efficiency |
100% (37/37) |
| MGI Phenotype |
PHENOTYPE: Mice homozygous for a knock-out allele display hypoactivity and a decreased excitatory synapse number in the hippocampal CA1 region, but show normal synaptic plasticity and hippocampus-dependent learning and memory. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 37 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A2m |
C |
T |
6: 121,618,246 (GRCm39) |
R180C |
probably damaging |
Het |
| B3galt9 |
C |
A |
2: 34,729,276 (GRCm39) |
S358R |
probably benign |
Het |
| Ces1b |
C |
A |
8: 93,791,619 (GRCm39) |
V327L |
probably benign |
Het |
| Cps1 |
C |
T |
1: 67,213,628 (GRCm39) |
R787* |
probably null |
Het |
| Dmrt2 |
C |
T |
19: 25,655,312 (GRCm39) |
P304S |
probably damaging |
Het |
| Dop1b |
A |
G |
16: 93,557,346 (GRCm39) |
D429G |
probably benign |
Het |
| Dync1h1 |
T |
A |
12: 110,616,282 (GRCm39) |
M3111K |
probably benign |
Het |
| Dync2h1 |
A |
G |
9: 7,037,699 (GRCm39) |
V3393A |
probably benign |
Het |
| Eml2 |
G |
A |
7: 18,935,088 (GRCm39) |
V432I |
probably damaging |
Het |
| Fam184a |
T |
C |
10: 53,517,063 (GRCm39) |
D1007G |
possibly damaging |
Het |
| Flt3 |
A |
C |
5: 147,312,545 (GRCm39) |
L132W |
probably damaging |
Het |
| Gm14322 |
G |
A |
2: 177,410,220 (GRCm39) |
S60N |
possibly damaging |
Het |
| Katnip |
C |
T |
7: 125,449,914 (GRCm39) |
R993C |
probably damaging |
Het |
| Kcnj16 |
T |
A |
11: 110,916,131 (GRCm39) |
Y264* |
probably null |
Het |
| Klkb1 |
T |
A |
8: 45,726,591 (GRCm39) |
I471F |
probably damaging |
Het |
| Mfsd4b5 |
T |
A |
10: 39,862,428 (GRCm39) |
T32S |
probably benign |
Het |
| Mtbp |
A |
G |
15: 55,430,645 (GRCm39) |
D234G |
probably damaging |
Het |
| Nfix |
T |
C |
8: 85,454,279 (GRCm39) |
T218A |
possibly damaging |
Het |
| Nsd3 |
A |
T |
8: 26,152,891 (GRCm39) |
E410D |
probably damaging |
Het |
| Or4g17 |
C |
T |
2: 111,209,504 (GRCm39) |
S53F |
possibly damaging |
Het |
| Or5aq7 |
A |
T |
2: 86,937,970 (GRCm39) |
S254T |
probably benign |
Het |
| Reln |
T |
C |
5: 22,101,838 (GRCm39) |
Y3364C |
probably damaging |
Het |
| Selplg |
G |
A |
5: 113,958,210 (GRCm39) |
P32L |
probably benign |
Het |
| Serpina1d |
A |
T |
12: 103,731,062 (GRCm39) |
H305Q |
probably benign |
Het |
| Skic8 |
A |
T |
9: 54,634,929 (GRCm39) |
I88N |
probably damaging |
Het |
| Skint8 |
G |
A |
4: 111,784,413 (GRCm39) |
C13Y |
probably benign |
Het |
| Smc4 |
G |
A |
3: 68,936,848 (GRCm39) |
V863I |
probably benign |
Het |
| Spdl1 |
T |
G |
11: 34,713,397 (GRCm39) |
N224T |
possibly damaging |
Het |
| Sprr1b |
T |
G |
3: 92,344,420 (GRCm39) |
Q152P |
possibly damaging |
Het |
| St6gal1 |
A |
G |
16: 23,140,405 (GRCm39) |
N192S |
probably benign |
Het |
| Tbc1d8 |
T |
C |
1: 39,445,903 (GRCm39) |
N96S |
probably damaging |
Het |
| Tbccd1 |
A |
T |
16: 22,640,874 (GRCm39) |
I501K |
probably damaging |
Het |
| Tmem161b |
C |
A |
13: 84,370,537 (GRCm39) |
|
probably benign |
Het |
| Unk |
T |
C |
11: 115,942,285 (GRCm39) |
I293T |
probably damaging |
Het |
| Vmn2r61 |
A |
G |
7: 41,926,139 (GRCm39) |
E548G |
probably damaging |
Het |
| Wdr97 |
A |
G |
15: 76,239,178 (GRCm39) |
D85G |
possibly damaging |
Het |
| Zeb2 |
A |
T |
2: 44,887,524 (GRCm39) |
V496E |
probably damaging |
Het |
|
| Other mutations in Lrfn4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
R0715:Lrfn4
|
UTSW |
19 |
4,662,668 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R1103:Lrfn4
|
UTSW |
19 |
4,663,299 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1629:Lrfn4
|
UTSW |
19 |
4,663,523 (GRCm39) |
missense |
possibly damaging |
0.60 |
|
R4406:Lrfn4
|
UTSW |
19 |
4,663,299 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4459:Lrfn4
|
UTSW |
19 |
4,662,662 (GRCm39) |
missense |
probably benign |
|
|
R5543:Lrfn4
|
UTSW |
19 |
4,662,191 (GRCm39) |
missense |
probably benign |
0.41 |
|
R6115:Lrfn4
|
UTSW |
19 |
4,663,937 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7626:Lrfn4
|
UTSW |
19 |
4,663,679 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7779:Lrfn4
|
UTSW |
19 |
4,663,715 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7968:Lrfn4
|
UTSW |
19 |
4,663,343 (GRCm39) |
missense |
probably benign |
0.06 |
|
R8008:Lrfn4
|
UTSW |
19 |
4,663,565 (GRCm39) |
missense |
probably benign |
0.21 |
|
R8356:Lrfn4
|
UTSW |
19 |
4,662,256 (GRCm39) |
missense |
probably benign |
0.44 |
|
R8482:Lrfn4
|
UTSW |
19 |
4,664,333 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9180:Lrfn4
|
UTSW |
19 |
4,663,353 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9507:Lrfn4
|
UTSW |
19 |
4,664,357 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9520:Lrfn4
|
UTSW |
19 |
4,664,237 (GRCm39) |
missense |
probably damaging |
0.99 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGGCTCACAGGAGAACTCTC -3'
(R):5'- TCAGTGGCAATCAACTGGG -3'
Sequencing Primer
(F):5'- GAGAACTCTCCCTCAGGCACTG -3'
(R):5'- GACGACTTCCTTGACAGTCTCGAG -3'
|
| Posted On |
2018-06-06 |
Incidental Mutation