Incidental Mutation 'R1251:Phf21a'
| ID |
151740 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Phf21a
|
| Ensembl Gene |
ENSMUSG00000058318 |
| Gene Name |
PHD finger protein 21A |
| Synonyms |
Braf35/HDAC complex (Bhc), 80kDa, Bhc80, PFTF1, D030065N23Rik |
| MMRRC Submission |
039318-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1251 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
2 |
| Chromosomal Location |
92014096-92195011 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 92189544 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Asparagine
at position 601
(S601N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000106924
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000044036]
[ENSMUST00000068702]
[ENSMUST00000090586]
[ENSMUST00000111290]
[ENSMUST00000111291]
[ENSMUST00000111292]
[ENSMUST00000111293]
[ENSMUST00000111294]
[ENSMUST00000111297]
[ENSMUST00000159961]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000044036
AA Change: S517N
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000038497
Gene: ENSMUSG00000058318
AA Change: S517N
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
29 |
62 |
N/A |
INTRINSIC |
|
low complexity region
|
85 |
129 |
N/A |
INTRINSIC |
|
low complexity region
|
165 |
186 |
N/A |
INTRINSIC |
|
AT_hook
|
350 |
362 |
4.28e-1 |
SMART |
|
low complexity region
|
369 |
381 |
N/A |
INTRINSIC |
|
PHD
|
415 |
458 |
3.12e-15 |
SMART |
|
RING
|
416 |
457 |
1.85e-1 |
SMART |
|
coiled coil region
|
482 |
527 |
N/A |
INTRINSIC |
|
low complexity region
|
575 |
595 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000068702
AA Change: S469N
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000070649
Gene: ENSMUSG00000058318
AA Change: S469N
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
29 |
62 |
N/A |
INTRINSIC |
|
low complexity region
|
85 |
128 |
N/A |
INTRINSIC |
|
low complexity region
|
164 |
185 |
N/A |
INTRINSIC |
|
PHD
|
367 |
410 |
3.12e-15 |
SMART |
|
RING
|
368 |
409 |
1.85e-1 |
SMART |
|
coiled coil region
|
434 |
479 |
N/A |
INTRINSIC |
|
low complexity region
|
527 |
547 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000090586
AA Change: S601N
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000088074
Gene: ENSMUSG00000058318
AA Change: S601N
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
29 |
62 |
N/A |
INTRINSIC |
|
low complexity region
|
85 |
128 |
N/A |
INTRINSIC |
|
low complexity region
|
249 |
270 |
N/A |
INTRINSIC |
|
AT_hook
|
434 |
446 |
4.28e-1 |
SMART |
|
low complexity region
|
453 |
465 |
N/A |
INTRINSIC |
|
PHD
|
499 |
542 |
3.12e-15 |
SMART |
|
RING
|
500 |
541 |
1.85e-1 |
SMART |
|
coiled coil region
|
566 |
611 |
N/A |
INTRINSIC |
|
low complexity region
|
659 |
679 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111290
AA Change: S572N
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000106921
Gene: ENSMUSG00000058318
AA Change: S572N
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
29 |
62 |
N/A |
INTRINSIC |
|
low complexity region
|
85 |
128 |
N/A |
INTRINSIC |
|
low complexity region
|
249 |
270 |
N/A |
INTRINSIC |
|
AT_hook
|
405 |
417 |
4.28e-1 |
SMART |
|
low complexity region
|
424 |
436 |
N/A |
INTRINSIC |
|
PHD
|
470 |
513 |
3.12e-15 |
SMART |
|
RING
|
471 |
512 |
1.85e-1 |
SMART |
|
coiled coil region
|
537 |
582 |
N/A |
INTRINSIC |
|
low complexity region
|
630 |
650 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111291
AA Change: S517N
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000106922
Gene: ENSMUSG00000058318
AA Change: S517N
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
29 |
62 |
N/A |
INTRINSIC |
|
low complexity region
|
85 |
129 |
N/A |
INTRINSIC |
|
low complexity region
|
165 |
186 |
N/A |
INTRINSIC |
|
AT_hook
|
350 |
362 |
4.28e-1 |
SMART |
|
low complexity region
|
369 |
381 |
N/A |
INTRINSIC |
|
PHD
|
415 |
458 |
3.12e-15 |
SMART |
|
RING
|
416 |
457 |
1.85e-1 |
SMART |
|
coiled coil region
|
482 |
527 |
N/A |
INTRINSIC |
|
low complexity region
|
575 |
595 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111292
AA Change: S469N
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000106923
Gene: ENSMUSG00000058318
AA Change: S469N
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
29 |
62 |
N/A |
INTRINSIC |
|
low complexity region
|
85 |
128 |
N/A |
INTRINSIC |
|
low complexity region
|
164 |
185 |
N/A |
INTRINSIC |
|
PHD
|
367 |
410 |
3.12e-15 |
SMART |
|
RING
|
368 |
409 |
1.85e-1 |
SMART |
|
coiled coil region
|
434 |
479 |
N/A |
INTRINSIC |
|
low complexity region
|
527 |
547 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111293
AA Change: S601N
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000106924
Gene: ENSMUSG00000058318
AA Change: S601N
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
29 |
62 |
N/A |
INTRINSIC |
|
low complexity region
|
85 |
128 |
N/A |
INTRINSIC |
|
low complexity region
|
249 |
270 |
N/A |
INTRINSIC |
|
AT_hook
|
434 |
446 |
4.28e-1 |
SMART |
|
low complexity region
|
453 |
465 |
N/A |
INTRINSIC |
|
PHD
|
499 |
542 |
3.12e-15 |
SMART |
|
RING
|
500 |
541 |
1.85e-1 |
SMART |
|
coiled coil region
|
566 |
611 |
N/A |
INTRINSIC |
|
low complexity region
|
659 |
679 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111294
AA Change: S554N
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000106925
Gene: ENSMUSG00000058318
AA Change: S554N
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
29 |
62 |
N/A |
INTRINSIC |
|
low complexity region
|
85 |
128 |
N/A |
INTRINSIC |
|
low complexity region
|
249 |
270 |
N/A |
INTRINSIC |
|
PHD
|
452 |
495 |
3.12e-15 |
SMART |
|
RING
|
453 |
494 |
1.85e-1 |
SMART |
|
coiled coil region
|
519 |
564 |
N/A |
INTRINSIC |
|
low complexity region
|
612 |
632 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111297
AA Change: S524N
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000106928
Gene: ENSMUSG00000058318
AA Change: S524N
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
29 |
62 |
N/A |
INTRINSIC |
|
low complexity region
|
85 |
129 |
N/A |
INTRINSIC |
|
low complexity region
|
248 |
269 |
N/A |
INTRINSIC |
|
PHD
|
422 |
465 |
3.12e-15 |
SMART |
|
RING
|
423 |
464 |
1.85e-1 |
SMART |
|
coiled coil region
|
489 |
534 |
N/A |
INTRINSIC |
|
low complexity region
|
582 |
602 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000159961
AA Change: S488N
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000123955
Gene: ENSMUSG00000058318
AA Change: S488N
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
1 |
34 |
N/A |
INTRINSIC |
|
low complexity region
|
57 |
100 |
N/A |
INTRINSIC |
|
low complexity region
|
136 |
157 |
N/A |
INTRINSIC |
|
AT_hook
|
321 |
333 |
4.28e-1 |
SMART |
|
low complexity region
|
340 |
352 |
N/A |
INTRINSIC |
|
PHD
|
386 |
429 |
3.12e-15 |
SMART |
|
RING
|
387 |
428 |
1.85e-1 |
SMART |
|
coiled coil region
|
453 |
498 |
N/A |
INTRINSIC |
|
low complexity region
|
546 |
566 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161044
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000161067
|
| SMART Domains |
Protein: ENSMUSP00000124255
Gene: ENSMUSG00000058318
| Domain | Start | End | E-Value | Type |
|---|
|
PHD
|
140 |
183 |
3.12e-15 |
SMART |
|
RING
|
141 |
182 |
1.85e-1 |
SMART |
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.3%
- 20x: 92.6%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The PHF21A gene encodes BHC80, a component of a BRAF35 (MIM 605535)/histone deacetylase (HDAC; see MIM 601241) complex (BHC) that mediates repression of neuron-specific genes through the cis-regulatory element known as repressor element-1 (RE1) or neural restrictive silencer (NRS) (Hakimi et al., 2002 [PubMed 12032298]).[supplied by OMIM, Nov 2010]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit neonatal lethality and insufficient milk-sucking behavior. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb10 |
C |
T |
8: 124,688,791 (GRCm39) |
G495D |
probably damaging |
Het |
| Acap2 |
A |
T |
16: 30,926,989 (GRCm39) |
Y509N |
probably damaging |
Het |
| Adcy9 |
T |
A |
16: 4,129,395 (GRCm39) |
E497V |
probably damaging |
Het |
| Bcat2 |
T |
G |
7: 45,225,410 (GRCm39) |
L56R |
probably damaging |
Het |
| Ccdc146 |
T |
C |
5: 21,498,370 (GRCm39) |
M952V |
probably benign |
Het |
| Ccdc39 |
T |
C |
3: 33,880,629 (GRCm39) |
K446R |
probably damaging |
Het |
| Cfap46 |
C |
T |
7: 139,181,181 (GRCm39) |
V2607I |
probably benign |
Het |
| Clec18a |
T |
C |
8: 111,808,270 (GRCm39) |
I54V |
possibly damaging |
Het |
| Coil |
A |
G |
11: 88,873,125 (GRCm39) |
E455G |
possibly damaging |
Het |
| Copg1 |
A |
T |
6: 87,866,989 (GRCm39) |
K75* |
probably null |
Het |
| Cyp2j12 |
G |
A |
4: 96,003,903 (GRCm39) |
Q238* |
probably null |
Het |
| Eif3i |
T |
C |
4: 129,487,178 (GRCm39) |
E229G |
probably damaging |
Het |
| Exoc2 |
T |
A |
13: 31,070,259 (GRCm39) |
N411Y |
probably benign |
Het |
| Eya2 |
T |
A |
2: 165,596,404 (GRCm39) |
M305K |
probably damaging |
Het |
| Faim |
C |
T |
9: 98,874,687 (GRCm39) |
T78M |
probably damaging |
Het |
| Fgg |
T |
A |
3: 82,920,287 (GRCm39) |
D355E |
probably benign |
Het |
| Foxn1 |
A |
G |
11: 78,249,611 (GRCm39) |
L638P |
probably damaging |
Het |
| Grid2ip |
A |
T |
5: 143,371,770 (GRCm39) |
E664D |
possibly damaging |
Het |
| Il1rn |
A |
G |
2: 24,235,582 (GRCm39) |
R21G |
probably damaging |
Het |
| Ilrun |
C |
T |
17: 28,005,044 (GRCm39) |
|
probably null |
Het |
| Inpp4b |
G |
A |
8: 82,617,382 (GRCm39) |
G220R |
probably benign |
Het |
| Irx6 |
A |
G |
8: 93,404,881 (GRCm39) |
S250G |
possibly damaging |
Het |
| Lyst |
T |
C |
13: 13,809,068 (GRCm39) |
I246T |
probably benign |
Het |
| Mcm3 |
G |
A |
1: 20,882,896 (GRCm39) |
Q353* |
probably null |
Het |
| Mfhas1 |
A |
G |
8: 36,058,207 (GRCm39) |
Y894C |
probably damaging |
Het |
| Mfsd13a |
T |
C |
19: 46,360,492 (GRCm39) |
L348P |
probably damaging |
Het |
| Necab1 |
A |
G |
4: 15,111,192 (GRCm39) |
|
probably null |
Het |
| Nectin3 |
A |
T |
16: 46,284,205 (GRCm39) |
S160T |
possibly damaging |
Het |
| Npc2 |
A |
G |
12: 84,807,658 (GRCm39) |
S67P |
probably damaging |
Het |
| Or5e1 |
T |
G |
7: 108,354,114 (GRCm39) |
F17C |
probably damaging |
Het |
| Or5m9b |
G |
A |
2: 85,905,164 (GRCm39) |
V27M |
probably benign |
Het |
| Pcnx3 |
A |
G |
19: 5,727,210 (GRCm39) |
F1108L |
probably benign |
Het |
| Pold1 |
C |
T |
7: 44,184,475 (GRCm39) |
V842I |
probably benign |
Het |
| Rabgap1 |
A |
G |
2: 37,433,246 (GRCm39) |
|
probably null |
Het |
| Setd1a |
T |
A |
7: 127,396,596 (GRCm39) |
|
probably benign |
Het |
| Sgo2a |
A |
T |
1: 58,039,121 (GRCm39) |
|
probably null |
Het |
| Sult2a8 |
T |
A |
7: 14,159,350 (GRCm39) |
K90* |
probably null |
Het |
| Tlr2 |
T |
C |
3: 83,745,576 (GRCm39) |
D169G |
possibly damaging |
Het |
| Tmem95 |
A |
G |
11: 69,767,655 (GRCm39) |
F153S |
probably benign |
Het |
| Tube1 |
G |
T |
10: 39,010,204 (GRCm39) |
G10* |
probably null |
Het |
| Vmn2r10 |
T |
C |
5: 109,143,890 (GRCm39) |
M687V |
probably benign |
Het |
| Zc3h8 |
G |
A |
2: 128,777,289 (GRCm39) |
P117S |
probably benign |
Het |
| Zeb1 |
T |
A |
18: 5,705,089 (GRCm39) |
D18E |
probably damaging |
Het |
|
| Other mutations in Phf21a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00331:Phf21a
|
APN |
2 |
92,178,374 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00826:Phf21a
|
APN |
2 |
92,174,881 (GRCm39) |
splice site |
probably benign |
|
|
IGL01859:Phf21a
|
APN |
2 |
92,158,701 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02124:Phf21a
|
APN |
2 |
92,179,767 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02724:Phf21a
|
APN |
2 |
92,190,592 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03155:Phf21a
|
APN |
2 |
92,150,611 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0308:Phf21a
|
UTSW |
2 |
92,161,122 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R1739:Phf21a
|
UTSW |
2 |
92,190,644 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R1775:Phf21a
|
UTSW |
2 |
92,160,860 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2013:Phf21a
|
UTSW |
2 |
92,058,828 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2064:Phf21a
|
UTSW |
2 |
92,157,422 (GRCm39) |
missense |
possibly damaging |
0.47 |
|
R2073:Phf21a
|
UTSW |
2 |
92,178,381 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4698:Phf21a
|
UTSW |
2 |
92,187,297 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4901:Phf21a
|
UTSW |
2 |
92,187,346 (GRCm39) |
nonsense |
probably null |
|
|
R5055:Phf21a
|
UTSW |
2 |
92,182,201 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5249:Phf21a
|
UTSW |
2 |
92,058,822 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5401:Phf21a
|
UTSW |
2 |
92,182,097 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R5770:Phf21a
|
UTSW |
2 |
92,182,199 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
R5969:Phf21a
|
UTSW |
2 |
92,051,956 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6008:Phf21a
|
UTSW |
2 |
92,182,097 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R6012:Phf21a
|
UTSW |
2 |
92,182,120 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6128:Phf21a
|
UTSW |
2 |
92,181,953 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R6354:Phf21a
|
UTSW |
2 |
92,179,282 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7075:Phf21a
|
UTSW |
2 |
92,190,724 (GRCm39) |
nonsense |
probably null |
|
|
R7117:Phf21a
|
UTSW |
2 |
92,189,502 (GRCm39) |
missense |
probably benign |
0.25 |
|
R7270:Phf21a
|
UTSW |
2 |
92,157,484 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7603:Phf21a
|
UTSW |
2 |
92,187,352 (GRCm39) |
missense |
probably benign |
0.08 |
|
R7708:Phf21a
|
UTSW |
2 |
92,157,511 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7946:Phf21a
|
UTSW |
2 |
92,189,512 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9788:Phf21a
|
UTSW |
2 |
92,181,978 (GRCm39) |
critical splice donor site |
probably null |
|
|
Z1177:Phf21a
|
UTSW |
2 |
92,061,059 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGACAGCAGACACTTTCAGGGC -3'
(R):5'- GGTGCAACTGGTATCCCATCTCTTC -3'
Sequencing Primer
(F):5'- CTGGTATCTTTGGTGAACAAAGCC -3'
(R):5'- TCTTCCCCAGCAGACTGAC -3'
|
| Posted On |
2014-01-29 |
Incidental Mutation