Mutagenetix > Incidental Mutation

Incidental Mutation 'R2073:Phf21a'

227301

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

040078-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2073 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

92014096-92195011 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 92178381 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 357 (D357G)

Ref Sequence

ENSEMBL: ENSMUSP00000106928 (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

probably damaging
Transcript: ENSMUST00000044036
AA Change: D303G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000038497
Gene: ENSMUSG00000058318
AA Change: D303G

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 damaging
Transcript: ENSMUST00000068702
AA Change: D302G

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000070649
Gene: ENSMUSG00000058318
AA Change: D302G

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: D387G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000088074
Gene: ENSMUSG00000058318
AA Change: D387G

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: D358G

PolyPhen 2 Score 0.466 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000106921
Gene: ENSMUSG00000058318
AA Change: D358G

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: D303G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000106922
Gene: ENSMUSG00000058318
AA Change: D303G

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 damaging
Transcript: ENSMUST00000111292
AA Change: D302G

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000106923
Gene: ENSMUSG00000058318
AA Change: D302G

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: ENSMUST00000111293
AA Change: D387G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000106924
Gene: ENSMUSG00000058318
AA Change: D387G

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: ENSMUST00000159961
AA Change: D274G

PolyPhen 2 Score 0.504 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000123955
Gene: ENSMUSG00000058318
AA Change: D274G

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: ENSMUST00000111297
AA Change: D357G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000106928
Gene: ENSMUSG00000058318
AA Change: D357G

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 damaging
Transcript: ENSMUST00000111294
AA Change: D387G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000106925
Gene: ENSMUSG00000058318
AA Change: D387G

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

unknown
Transcript: ENSMUST00000161067
AA Change: D74G

SMART Domains

Protein: ENSMUSP00000124255
Gene: ENSMUSG00000058318
AA Change: D74G

Domain	Start	End	E-Value	Type
PHD	140	183	3.12e-15	SMART
RING	141	182	1.85e-1	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161044

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.2%

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: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310057M21Rik	T	C	7: 130,959,242 (GRCm39)	R153G	probably benign	Het
5730596B20Rik	C	A	6: 52,155,962 (GRCm39)	Y9*	probably null	Het
Aco1	G	A	4: 40,183,605 (GRCm39)	G508S	probably damaging	Het
Acot3	A	G	12: 84,100,230 (GRCm39)	H2R	possibly damaging	Het
Adamts13	T	A	2: 26,896,326 (GRCm39)	C1240S	probably damaging	Het
Adra1b	T	C	11: 43,726,698 (GRCm39)	N73S	probably damaging	Het
Aebp2	G	A	6: 140,579,420 (GRCm39)	S219N	probably benign	Het
Akap8l	C	T	17: 32,551,457 (GRCm39)	R511H	probably damaging	Het
Ank	T	C	15: 27,565,108 (GRCm39)	S270P	probably benign	Het
Ankle1	G	A	8: 71,861,973 (GRCm39)	R492H	possibly damaging	Het
Ankub1	G	A	3: 57,599,713 (GRCm39)	H19Y	possibly damaging	Het
Anln	C	A	9: 22,244,464 (GRCm39)	W1083L	probably benign	Het
Apaf1	G	T	10: 90,867,556 (GRCm39)	S763*	probably null	Het
Apba3	A	G	10: 81,105,128 (GRCm39)	T134A	probably benign	Het
Armh3	A	T	19: 45,953,820 (GRCm39)	I188K	probably damaging	Het
Bod1l	C	T	5: 41,976,532 (GRCm39)	S1594N	probably benign	Het
C7	T	C	15: 5,019,910 (GRCm39)	M746V	probably benign	Het
Cdkn2a	T	A	4: 89,212,730 (GRCm39)	I11F	possibly damaging	Het
Cideb	T	C	14: 55,992,617 (GRCm39)	M100V	possibly damaging	Het
Cntnap5c	T	C	17: 58,612,547 (GRCm39)	L862P	possibly damaging	Het
Coch	A	T	12: 51,649,472 (GRCm39)	D261V	probably benign	Het
Cyp2ab1	A	G	16: 20,132,639 (GRCm39)	F220L	possibly damaging	Het
Ddx10	A	T	9: 53,151,805 (GRCm39)	D73E	probably benign	Het
Dgkg	A	G	16: 22,384,067 (GRCm39)	F462S	probably damaging	Het
Dlgap3	C	T	4: 127,089,159 (GRCm39)	H252Y	probably damaging	Het
Dmd	G	C	X: 83,356,089 (GRCm39)	A2257P	probably benign	Het
Dnaaf6rt	A	G	1: 31,262,077 (GRCm39)	S20G	probably benign	Het
Dnai4	G	A	4: 102,907,390 (GRCm39)	T632M	probably damaging	Het
Dtnb	A	G	12: 3,831,273 (GRCm39)	T658A	probably benign	Het
Duox2	T	A	2: 122,125,639 (GRCm39)	S323C	probably damaging	Het
Dync1h1	T	A	12: 110,581,026 (GRCm39)	I251N	probably damaging	Het
Eml5	A	G	12: 98,768,705 (GRCm39)	S1457P	probably damaging	Het
Fam114a1	T	A	5: 65,153,247 (GRCm39)		probably null	Het
Fcho1	A	T	8: 72,163,133 (GRCm39)	L632Q	probably damaging	Het
Gm12695	T	C	4: 96,612,182 (GRCm39)	Y527C	possibly damaging	Het
Gm16223	T	C	5: 42,371,942 (GRCm39)	C111R	unknown	Het
H2-Q4	T	A	17: 35,599,378 (GRCm39)	S154T	possibly damaging	Het
Hhat	A	G	1: 192,409,687 (GRCm39)	F125L	possibly damaging	Het
Ier5l	T	A	2: 30,363,068 (GRCm39)	D319V	probably damaging	Het
Kif5a	T	C	10: 127,081,238 (GRCm39)	D232G	probably damaging	Het
M1ap	A	G	6: 82,958,863 (GRCm39)	I165V	probably benign	Het
Map2k4	A	C	11: 65,584,282 (GRCm39)	F334V	probably damaging	Het
Mmp19	G	A	10: 128,630,848 (GRCm39)	R156H	probably damaging	Het
Mpped2	T	A	2: 106,575,147 (GRCm39)	Y77*	probably null	Het
Nhs	T	A	X: 160,625,717 (GRCm39)	H544L	probably damaging	Het
Nr4a1	C	A	15: 101,171,948 (GRCm39)	H541N	probably damaging	Het
Or4a74	A	G	2: 89,439,822 (GRCm39)	V208A	probably benign	Het
Or5b122	A	T	19: 13,562,965 (GRCm39)	Q99L	probably damaging	Het
Pak6	A	C	2: 118,519,332 (GRCm39)	N17T	probably damaging	Het
Pcnt	T	A	10: 76,216,214 (GRCm39)	T2225S	possibly damaging	Het
Pdzd2	A	G	15: 12,385,905 (GRCm39)	L955P	probably damaging	Het
Pkhd1l1	G	T	15: 44,422,035 (GRCm39)	A3102S	probably damaging	Het
Plch2	A	T	4: 155,074,366 (GRCm39)	L754Q	probably damaging	Het
Plekhd1	A	G	12: 80,768,066 (GRCm39)	N335D	probably benign	Het
Pole	C	A	5: 110,473,417 (GRCm39)	T1737N	probably damaging	Het
Potefam1	T	C	2: 111,030,763 (GRCm39)	E382G	probably damaging	Het
Pramel6	G	A	2: 87,339,088 (GRCm39)	S96N	probably damaging	Het
Prdm14	A	C	1: 13,195,954 (GRCm39)	Y36D	possibly damaging	Het
Psg27	T	C	7: 18,294,342 (GRCm39)	D355G	probably damaging	Het
Rfc1	A	T	5: 65,459,282 (GRCm39)	D225E	probably damaging	Het
Sec16a	A	G	2: 26,330,251 (GRCm39)	I588T	probably damaging	Het
Setd6	G	A	8: 96,443,416 (GRCm39)	V60M	probably damaging	Het
Sgk3	A	G	1: 9,961,649 (GRCm39)	I432V	probably benign	Het
Six2	A	G	17: 85,994,933 (GRCm39)	S150P	probably damaging	Het
Slc1a6	T	C	10: 78,635,964 (GRCm39)	V343A	possibly damaging	Het
Slc43a3	T	C	2: 84,774,956 (GRCm39)		probably null	Het
Smc3	A	G	19: 53,619,964 (GRCm39)	D620G	probably benign	Het
Smg6	C	G	11: 74,821,120 (GRCm39)	P464A	probably damaging	Het
Sox11	T	C	12: 27,392,278 (GRCm39)	T44A	possibly damaging	Het
Spata22	A	G	11: 73,227,052 (GRCm39)	R89G	possibly damaging	Het
Spmip6	A	G	4: 41,507,519 (GRCm39)		probably null	Het
Stk3	T	C	15: 34,959,195 (GRCm39)	M256V	possibly damaging	Het
Syne2	A	G	12: 76,062,353 (GRCm39)	D4226G	possibly damaging	Het
Tecpr2	T	C	12: 110,934,863 (GRCm39)	S1370P	possibly damaging	Het
Tek	A	G	4: 94,715,966 (GRCm39)	I463V	probably benign	Het
Trib1	T	A	15: 59,526,189 (GRCm39)	I253N	probably damaging	Het
Triobp	G	T	15: 78,858,095 (GRCm39)	G1232V	probably damaging	Het
Trpm6	G	A	19: 18,853,406 (GRCm39)	V1809M	probably damaging	Het
Tsc22d4	A	G	5: 137,760,749 (GRCm39)	K57E	possibly damaging	Het
Vmn2r109	T	A	17: 20,784,974 (GRCm39)	K15N	probably benign	Het
Wnt9a	A	G	11: 59,222,055 (GRCm39)	N318D	probably damaging	Het
Wwp1	A	G	4: 19,662,181 (GRCm39)	V138A	possibly damaging	Het
Zfp37	A	T	4: 62,109,945 (GRCm39)	M411K	probably damaging	Het
Zfp715	T	A	7: 42,960,544 (GRCm39)	T16S	probably benign	Het
Zfp932	A	G	5: 110,157,684 (GRCm39)	T461A	possibly damaging	Het
Zscan29	A	T	2: 120,991,336 (GRCm39)	C817*	probably null	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
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'- CTGCATGCTTTCCACTATAGATACC -3'
(R):5'- AGGGCCCACACATTACATGG -3'

Sequencing Primer
(F):5'- GATTCTTCTGAGCAAAAATCCAAAC -3'
(R):5'- CACATTACATGGACGGGGCAATTC -3'

Posted On

2014-09-17