Incidental Mutation 'R5401:Phf21a'
| ID |
429968 |
| 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 |
042972-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5401 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
92014096-92195011 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 92182097 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Lysine
at position 342
(T342K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000123955
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000044036]
[ENSMUST00000068702]
[ENSMUST00000090586]
[ENSMUST00000111290]
[ENSMUST00000111291]
[ENSMUST00000111292]
[ENSMUST00000111293]
[ENSMUST00000159961]
[ENSMUST00000111297]
[ENSMUST00000111294]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000044036
AA Change: T371K
PolyPhen 2
Score 0.673 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000038497
Gene: ENSMUSG00000058318
AA Change: T371K
| 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
|
| SMART Domains |
Protein: ENSMUSP00000070649
Gene: ENSMUSG00000058318
| 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: T455K
PolyPhen 2
Score 0.196 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000088074
Gene: ENSMUSG00000058318
AA Change: T455K
| 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: T426K
PolyPhen 2
Score 0.116 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000106921
Gene: ENSMUSG00000058318
AA Change: T426K
| 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 |
possibly damaging
Transcript: ENSMUST00000111291
AA Change: T371K
PolyPhen 2
Score 0.673 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000106922
Gene: ENSMUSG00000058318
AA Change: T371K
| 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
|
| SMART Domains |
Protein: ENSMUSP00000106923
Gene: ENSMUSG00000058318
| 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: T455K
PolyPhen 2
Score 0.196 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000106924
Gene: ENSMUSG00000058318
AA Change: T455K
| 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 |
noncoding transcript
Transcript: ENSMUST00000161044
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000159961
AA Change: T342K
PolyPhen 2
Score 0.712 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000123955
Gene: ENSMUSG00000058318
AA Change: T342K
| 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 |
probably benign
Transcript: ENSMUST00000111297
|
| SMART Domains |
Protein: ENSMUSP00000106928
Gene: ENSMUSG00000058318
| 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: ENSMUST00000111294
|
| SMART Domains |
Protein: ENSMUSP00000106925
Gene: ENSMUSG00000058318
| 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: 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 |
|
| Meta Mutation Damage Score |
0.0736 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.7%
- 10x: 97.3%
- 20x: 95.4%
|
| Validation Efficiency |
97% (66/68) |
| 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: 53 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700001J11Rik |
A |
G |
9: 39,962,338 (GRCm39) |
|
noncoding transcript |
Het |
| 1700025H01Rik |
G |
T |
16: 30,018,801 (GRCm39) |
|
noncoding transcript |
Het |
| 9330159F19Rik |
T |
C |
10: 29,101,136 (GRCm39) |
V503A |
probably benign |
Het |
| Acacb |
A |
G |
5: 114,347,914 (GRCm39) |
N995S |
possibly damaging |
Het |
| Anapc4 |
A |
G |
5: 53,020,991 (GRCm39) |
K630R |
probably benign |
Het |
| Ankrd13a |
A |
C |
5: 114,930,234 (GRCm39) |
Q206H |
probably damaging |
Het |
| Ano10 |
A |
T |
9: 122,090,356 (GRCm39) |
L319Q |
probably damaging |
Het |
| Camkk2 |
T |
A |
5: 122,884,398 (GRCm39) |
D341V |
probably damaging |
Het |
| Ccdc88a |
A |
G |
11: 29,413,279 (GRCm39) |
I606V |
probably benign |
Het |
| Cdv3 |
G |
T |
9: 103,242,316 (GRCm39) |
|
probably benign |
Het |
| Cep97 |
A |
G |
16: 55,745,315 (GRCm39) |
V155A |
probably benign |
Het |
| Cmya5 |
T |
C |
13: 93,228,476 (GRCm39) |
E2204G |
probably damaging |
Het |
| Cracr2b |
A |
G |
7: 141,046,136 (GRCm39) |
*395W |
probably null |
Het |
| Defa27 |
A |
G |
8: 21,805,710 (GRCm39) |
E50G |
possibly damaging |
Het |
| Dnah7a |
A |
G |
1: 53,670,812 (GRCm39) |
I480T |
probably benign |
Het |
| Ep400 |
C |
A |
5: 110,831,037 (GRCm39) |
D2210Y |
unknown |
Het |
| Fam170a |
T |
A |
18: 50,413,618 (GRCm39) |
S28T |
probably benign |
Het |
| Fancc |
C |
A |
13: 63,550,767 (GRCm39) |
K18N |
probably damaging |
Het |
| Flt4 |
AC |
ACC |
11: 49,541,861 (GRCm39) |
|
probably null |
Het |
| Fndc8 |
T |
G |
11: 82,788,676 (GRCm39) |
S169A |
possibly damaging |
Het |
| Get3 |
A |
T |
8: 85,745,173 (GRCm39) |
I298N |
possibly damaging |
Het |
| Herc1 |
T |
C |
9: 66,409,338 (GRCm39) |
Y4688H |
probably damaging |
Het |
| Ighv11-2 |
A |
T |
12: 114,011,959 (GRCm39) |
D85E |
possibly damaging |
Het |
| Kat14 |
T |
C |
2: 144,231,180 (GRCm39) |
F196L |
possibly damaging |
Het |
| Kctd19 |
C |
T |
8: 106,109,617 (GRCm39) |
V942I |
probably benign |
Het |
| Llgl1 |
A |
G |
11: 60,597,297 (GRCm39) |
S249G |
probably benign |
Het |
| Map1a |
T |
C |
2: 121,130,153 (GRCm39) |
V323A |
probably damaging |
Het |
| Or4m1 |
C |
A |
14: 50,557,566 (GRCm39) |
C242F |
probably damaging |
Het |
| Piezo2 |
T |
A |
18: 63,217,811 (GRCm39) |
D1122V |
possibly damaging |
Het |
| Pklr |
A |
G |
3: 89,049,173 (GRCm39) |
Y173C |
probably damaging |
Het |
| Plcz1 |
G |
T |
6: 139,938,778 (GRCm39) |
|
probably null |
Het |
| Polr3a |
T |
C |
14: 24,505,009 (GRCm39) |
I1084V |
possibly damaging |
Het |
| Prom1 |
A |
T |
5: 44,158,147 (GRCm39) |
Y845N |
probably damaging |
Het |
| Qng1 |
C |
A |
13: 58,530,405 (GRCm39) |
A202S |
probably benign |
Het |
| Ret |
A |
T |
6: 118,158,936 (GRCm39) |
S159T |
probably benign |
Het |
| Rfx1 |
C |
A |
8: 84,793,005 (GRCm39) |
|
probably null |
Het |
| Scp2 |
A |
T |
4: 108,001,976 (GRCm39) |
|
probably null |
Het |
| Sh3bp5 |
C |
A |
14: 31,099,452 (GRCm39) |
R265L |
probably benign |
Het |
| Slc22a30 |
G |
A |
19: 8,321,757 (GRCm39) |
Q436* |
probably null |
Het |
| Smad5 |
T |
C |
13: 56,875,282 (GRCm39) |
F157L |
probably benign |
Het |
| Smarcc2 |
C |
A |
10: 128,301,373 (GRCm39) |
D210E |
probably damaging |
Het |
| Sptlc3 |
T |
C |
2: 139,478,643 (GRCm39) |
L534P |
possibly damaging |
Het |
| Srrm1 |
A |
G |
4: 135,051,380 (GRCm39) |
|
probably benign |
Het |
| Srsf11 |
C |
T |
3: 157,728,981 (GRCm39) |
|
probably benign |
Het |
| Sugct |
T |
A |
13: 17,032,455 (GRCm39) |
Q432H |
probably damaging |
Het |
| Tex9 |
A |
T |
9: 72,394,060 (GRCm39) |
|
probably null |
Het |
| Tsc1 |
C |
A |
2: 28,576,920 (GRCm39) |
S1073* |
probably null |
Het |
| Vmn1r72 |
T |
C |
7: 11,403,843 (GRCm39) |
S202G |
probably damaging |
Het |
| Vmn2r55 |
A |
G |
7: 12,385,871 (GRCm39) |
V703A |
probably benign |
Het |
| Vmn2r67 |
A |
T |
7: 84,785,765 (GRCm39) |
Y747N |
probably damaging |
Het |
| Zcchc4 |
A |
G |
5: 52,964,419 (GRCm39) |
I292V |
probably benign |
Het |
| Zfp998 |
T |
C |
13: 66,579,722 (GRCm39) |
R254G |
probably benign |
Het |
| Zswim2 |
C |
T |
2: 83,755,589 (GRCm39) |
G104E |
possibly 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 |
|
R1251:Phf21a
|
UTSW |
2 |
92,189,544 (GRCm39) |
missense |
probably benign |
0.00 |
|
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 |
|
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'- AGCTATGCTCCAAGACTCCC -3'
(R):5'- GCACAGGACAATGGCTTTCC -3'
Sequencing Primer
(F):5'- GGATTCATGTAGTCGTTTCTAATGAC -3'
(R):5'- TCCCATGTGAGCTCTCAGAG -3'
|
| Posted On |
2016-09-06 |
Incidental Mutation