Incidental Mutation 'R6012:Phf21a'
ID |
479789 |
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 |
044188-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R6012 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
2 |
Chromosomal Location |
92014096-92195011 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
G to A
at 92182120 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Asparagine
at position 463
(D463N)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000106924
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000044036]
[ENSMUST00000068702]
[ENSMUST00000090586]
[ENSMUST00000111290]
[ENSMUST00000111291]
[ENSMUST00000111292]
[ENSMUST00000159961]
[ENSMUST00000111293]
[ENSMUST00000111294]
[ENSMUST00000111297]
|
AlphaFold |
no structure available at present |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000044036
AA Change: D379N
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
SMART Domains |
Protein: ENSMUSP00000038497 Gene: ENSMUSG00000058318 AA Change: D379N
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 damaging
Transcript: ENSMUST00000090586
AA Change: D463N
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
SMART Domains |
Protein: ENSMUSP00000088074 Gene: ENSMUSG00000058318 AA Change: D463N
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 |
possibly damaging
Transcript: ENSMUST00000111290
AA Change: D434N
PolyPhen 2
Score 0.662 (Sensitivity: 0.86; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000106921 Gene: ENSMUSG00000058318 AA Change: D434N
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 damaging
Transcript: ENSMUST00000111291
AA Change: D379N
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
SMART Domains |
Protein: ENSMUSP00000106922 Gene: ENSMUSG00000058318 AA Change: D379N
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 |
possibly damaging
Transcript: ENSMUST00000159961
AA Change: D350N
PolyPhen 2
Score 0.935 (Sensitivity: 0.80; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000123955 Gene: ENSMUSG00000058318 AA Change: D350N
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 damaging
Transcript: ENSMUST00000111293
AA Change: D463N
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
SMART Domains |
Protein: ENSMUSP00000106924 Gene: ENSMUSG00000058318 AA Change: D463N
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 |
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 |
|
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: 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 |
|
Meta Mutation Damage Score |
0.0841 |
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.5%
- 20x: 92.4%
|
Validation Efficiency |
100% (55/55) |
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 |
Abat |
T |
A |
16: 8,400,691 (GRCm39) |
Y97N |
probably damaging |
Het |
Adrm1b |
C |
A |
3: 92,336,791 (GRCm39) |
|
probably null |
Het |
Akr1b10 |
A |
T |
6: 34,364,715 (GRCm39) |
I59F |
probably damaging |
Het |
Als2 |
A |
T |
1: 59,224,374 (GRCm39) |
D1076E |
probably damaging |
Het |
Bank1 |
T |
C |
3: 135,919,598 (GRCm39) |
D266G |
probably benign |
Het |
Bmp2k |
T |
A |
5: 97,211,467 (GRCm39) |
|
probably null |
Het |
Cdc42bpa |
A |
G |
1: 179,892,655 (GRCm39) |
Y273C |
probably damaging |
Het |
Chfr |
G |
T |
5: 110,292,517 (GRCm39) |
|
probably null |
Het |
Dapk1 |
A |
T |
13: 60,909,476 (GRCm39) |
Q1363L |
probably benign |
Het |
Ddx23 |
A |
T |
15: 98,548,651 (GRCm39) |
D352E |
possibly damaging |
Het |
Ect2 |
T |
C |
3: 27,152,474 (GRCm39) |
|
probably benign |
Het |
Efcab10 |
A |
C |
12: 33,448,592 (GRCm39) |
D107A |
probably damaging |
Het |
Fcgr4 |
G |
A |
1: 170,853,233 (GRCm39) |
G146D |
possibly damaging |
Het |
Fgd5 |
A |
G |
6: 91,966,322 (GRCm39) |
T694A |
possibly damaging |
Het |
Ghr |
T |
C |
15: 3,370,409 (GRCm39) |
D152G |
probably damaging |
Het |
Gli2 |
A |
C |
1: 118,765,445 (GRCm39) |
L902R |
probably damaging |
Het |
Glis2 |
G |
A |
16: 4,429,172 (GRCm39) |
G125D |
possibly damaging |
Het |
Gmcl1 |
A |
G |
6: 86,698,394 (GRCm39) |
Y168H |
probably damaging |
Het |
Golga4 |
A |
G |
9: 118,388,764 (GRCm39) |
K1962R |
possibly damaging |
Het |
Hebp1 |
T |
A |
6: 135,145,055 (GRCm39) |
E14V |
probably damaging |
Het |
Hhla1 |
A |
C |
15: 65,820,339 (GRCm39) |
I137S |
probably damaging |
Het |
Hivep1 |
A |
G |
13: 42,337,934 (GRCm39) |
H2671R |
possibly damaging |
Het |
Hltf |
A |
G |
3: 20,113,098 (GRCm39) |
Y19C |
probably damaging |
Het |
Hsd3b2 |
A |
T |
3: 98,619,333 (GRCm39) |
M204K |
probably benign |
Het |
Hspa4l |
A |
T |
3: 40,736,031 (GRCm39) |
I551F |
probably benign |
Het |
Itpkc |
A |
T |
7: 26,927,490 (GRCm39) |
D141E |
probably damaging |
Het |
Kcnc3 |
A |
G |
7: 44,248,296 (GRCm39) |
D757G |
probably benign |
Het |
Mettl16 |
A |
T |
11: 74,678,474 (GRCm39) |
Y141F |
probably damaging |
Het |
Mfng |
G |
A |
15: 78,640,840 (GRCm39) |
R302C |
probably damaging |
Het |
Mogs |
T |
A |
6: 83,094,363 (GRCm39) |
S393R |
probably damaging |
Het |
Mrps28 |
A |
G |
3: 8,965,044 (GRCm39) |
|
probably null |
Het |
Nfat5 |
T |
C |
8: 108,093,765 (GRCm39) |
S150P |
probably benign |
Het |
Or2w1 |
T |
C |
13: 21,316,978 (GRCm39) |
V11A |
probably benign |
Het |
Or7d10 |
A |
T |
9: 19,832,237 (GRCm39) |
H244L |
probably damaging |
Het |
Pcdh12 |
A |
G |
18: 38,416,805 (GRCm39) |
S107P |
probably damaging |
Het |
Picalm |
A |
C |
7: 89,844,908 (GRCm39) |
I567L |
probably benign |
Het |
Pla2g4a |
T |
A |
1: 149,808,428 (GRCm39) |
D5V |
possibly damaging |
Het |
Sspo |
C |
T |
6: 48,428,305 (GRCm39) |
T222M |
probably benign |
Het |
Stard9 |
T |
C |
2: 120,535,067 (GRCm39) |
S3775P |
probably damaging |
Het |
Stk31 |
A |
T |
6: 49,446,243 (GRCm39) |
D982V |
probably damaging |
Het |
Tas2r113 |
C |
T |
6: 132,870,644 (GRCm39) |
T224I |
probably damaging |
Het |
Tbc1d15 |
T |
C |
10: 115,055,112 (GRCm39) |
D310G |
probably damaging |
Het |
Tcf12 |
G |
T |
9: 71,766,229 (GRCm39) |
T468K |
possibly damaging |
Het |
Tenm4 |
A |
G |
7: 96,171,640 (GRCm39) |
|
probably benign |
Het |
Tet2 |
A |
G |
3: 133,172,542 (GRCm39) |
Y1907H |
possibly damaging |
Het |
Thsd7a |
T |
C |
6: 12,379,388 (GRCm39) |
|
probably null |
Het |
Tln1 |
T |
A |
4: 43,539,508 (GRCm39) |
T1605S |
probably benign |
Het |
Trp53bp1 |
T |
C |
2: 121,087,083 (GRCm39) |
Y191C |
probably benign |
Het |
Ugcg |
T |
A |
4: 59,220,272 (GRCm39) |
I355N |
probably damaging |
Het |
Vmn1r21 |
A |
T |
6: 57,820,891 (GRCm39) |
D184E |
probably damaging |
Het |
Vsig10l |
T |
A |
7: 43,117,439 (GRCm39) |
D575E |
probably damaging |
Het |
Zan |
G |
A |
5: 137,462,791 (GRCm39) |
T796I |
unknown |
Het |
Zfp639 |
A |
G |
3: 32,573,271 (GRCm39) |
D61G |
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 |
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 |
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 |
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'- TGCTAGCCAATGAGGAACAC -3'
(R):5'- AAGCTGCCTGGCAAGGTATG -3'
Sequencing Primer
(F):5'- CACTGGCCAAAGGTATGTAAGATC -3'
(R):5'- TGCTATTCCAGGGCTAGCAAG -3'
|
Posted On |
2017-06-26 |