Mutagenetix > Incidental Mutation

Incidental Mutation 'R7603:Phf21a'

588102

Institutional Source

Beutler Lab

Gene Symbol

Phf21a

Ensembl Gene

ENSMUSG00000058318

Gene Name

PHD finger protein 21A

Synonyms

PFTF1, Bhc80, Braf35/HDAC complex (Bhc), 80kDa, D030065N23Rik

MMRRC Submission

045713-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7603 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

92093117-92364666 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 92357007 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Serine at position 540 (R540S)

Ref Sequence

ENSEMBL: ENSMUSP00000088074 (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: R456S

PolyPhen 2 Score 0.434 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000038497
Gene: ENSMUSG00000058318
AA Change: R456S

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: R408S

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000070649
Gene: ENSMUSG00000058318
AA Change: R408S

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: R540S

PolyPhen 2 Score 0.084 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000088074
Gene: ENSMUSG00000058318
AA Change: R540S

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: R511S

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000106921
Gene: ENSMUSG00000058318
AA Change: R511S

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: R456S

PolyPhen 2 Score 0.434 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000106922
Gene: ENSMUSG00000058318
AA Change: R456S

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: R408S

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000106923
Gene: ENSMUSG00000058318
AA Change: R408S

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: R540S

PolyPhen 2 Score 0.084 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000106924
Gene: ENSMUSG00000058318
AA Change: R540S

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: R493S

PolyPhen 2 Score 0.038 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000106925
Gene: ENSMUSG00000058318
AA Change: R493S

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: R463S

PolyPhen 2 Score 0.084 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000106928
Gene: ENSMUSG00000058318
AA Change: R463S

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: R427S

PolyPhen 2 Score 0.167 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000123955
Gene: ENSMUSG00000058318
AA Change: R427S

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

SMART Domains

Protein: ENSMUSP00000124255
Gene: ENSMUSG00000058318
AA Change: R180S

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

98% (47/48)

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: 47 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610010F05Rik	T	C	11: 23,566,191	T709A	probably benign	Het
Abca6	T	C	11: 110,180,258	K1536E	possibly damaging	Het
Abhd16a	T	A	17: 35,101,960		probably null	Het
Actrt3	C	T	3: 30,598,547	A133T	probably benign	Het
Adcy10	C	T	1: 165,564,237	R1329W	probably damaging	Het
Apol7b	T	C	15: 77,423,456	M280V	possibly damaging	Het
Canx	A	T	11: 50,311,628	D50E	probably benign	Het
Csmd1	A	T	8: 16,288,682	D470E	probably damaging	Het
Cyp2c23	C	T	19: 44,014,930	D269N	probably damaging	Het
Ddah1	T	C	3: 145,759,019	V53A	probably benign	Het
Epha7	C	T	4: 28,871,937	S422L	probably benign	Het
Fastkd5	A	G	2: 130,615,041	V543A	possibly damaging	Het
Fggy	G	A	4: 95,769,506	G295R	probably damaging	Het
Frs2	T	C	10: 117,074,063	T465A	probably benign	Het
Glipr1	A	T	10: 111,988,832	N156K	probably benign	Het
Gnpnat1	C	T	14: 45,384,617	V40I	probably benign	Het
H2-Q7	T	C	17: 35,439,963	L130P	probably damaging	Het
Herc1	T	A	9: 66,451,383	L86*	probably null	Het
Hspg2	T	C	4: 137,548,368	L2778P	probably damaging	Het
Hspg2	T	A	4: 137,557,192	I3487N	possibly damaging	Het
Htra4	T	G	8: 25,025,700	I441L	probably benign	Het
Ints7	A	T	1: 191,596,224	H203L	probably damaging	Het
Lama2	T	C	10: 27,266,680	T601A	possibly damaging	Het
Lin7b	T	C	7: 45,368,432		probably benign	Het
Lmbr1l	G	A	15: 98,908,691	Q280*	probably null	Het
Lpin3	G	T	2: 160,903,754		probably null	Het
Map1lc3b	A	T	8: 121,593,529	H27L	possibly damaging	Het
Mfsd14a	C	A	3: 116,633,883	V369F	probably damaging	Het
Ndufa12	C	T	10: 94,220,779	A123V	probably benign	Het
Nek9	A	G	12: 85,303,514	F929L	probably benign	Het
Nup210	A	T	6: 91,076,697	D279E	probably benign	Het
Olfr553	A	G	7: 102,614,938	V17A	probably benign	Het
Parp1	T	C	1: 180,600,212		probably null	Het
Phc3	T	C	3: 30,907,452	I944V	probably damaging	Het
Phf20	C	T	2: 156,302,851	A793V	probably benign	Het
Pogk	A	G	1: 166,401,911	C124R	probably benign	Het
Rif1	C	T	2: 52,076,175	S93L	probably damaging	Het
Sele	A	G	1: 164,049,515	E120G	probably damaging	Het
Slc4a1ap	T	C	5: 31,546,195	L49P		Het
Snap47	T	C	11: 59,428,547	D255G	probably damaging	Het
Tcstv3	T	C	13: 120,317,610	V15A	probably damaging	Het
Tmcc1	A	T	6: 116,043,131	Y453*	probably null	Het
Tpsg1	G	T	17: 25,373,210	G86V	probably damaging	Het
Urb1	CACTTAC	CAC	16: 90,772,573		probably benign	Het
Usp20	T	A	2: 31,011,474	V459E	probably damaging	Het
Vmn1r202	A	T	13: 22,501,620	L209Q	probably damaging	Het
Vps13b	T	C	15: 35,576,439	S998P	probably damaging	Het

Other mutations in Phf21a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00331:Phf21a	APN	2	92348029	missense	probably damaging	1.00
IGL00826:Phf21a	APN	2	92344536	splice site	probably benign
IGL01859:Phf21a	APN	2	92328356	missense	probably damaging	1.00
IGL02124:Phf21a	APN	2	92349422	missense	probably damaging	1.00
IGL02724:Phf21a	APN	2	92360247	missense	probably damaging	1.00
IGL03155:Phf21a	APN	2	92320266	missense	probably damaging	0.99
R0308:Phf21a	UTSW	2	92330777	missense	possibly damaging	0.86
R1251:Phf21a	UTSW	2	92359199	missense	probably benign	0.00
R1739:Phf21a	UTSW	2	92360299	missense	possibly damaging	0.95
R1775:Phf21a	UTSW	2	92330515	missense	probably damaging	1.00
R2013:Phf21a	UTSW	2	92228483	critical splice donor site	probably null
R2064:Phf21a	UTSW	2	92327077	missense	possibly damaging	0.47
R2073:Phf21a	UTSW	2	92348036	missense	probably damaging	1.00
R4698:Phf21a	UTSW	2	92356952	missense	probably damaging	1.00
R4901:Phf21a	UTSW	2	92357001	nonsense	probably null
R5055:Phf21a	UTSW	2	92351856	missense	probably damaging	1.00
R5249:Phf21a	UTSW	2	92228477	missense	probably damaging	1.00
R5401:Phf21a	UTSW	2	92351752	missense	possibly damaging	0.71
R5770:Phf21a	UTSW	2	92351854	missense	possibly damaging	0.52
R5969:Phf21a	UTSW	2	92221611	missense	probably damaging	0.98
R6008:Phf21a	UTSW	2	92351752	missense	possibly damaging	0.71
R6012:Phf21a	UTSW	2	92351775	missense	probably damaging	1.00
R6128:Phf21a	UTSW	2	92351608	critical splice acceptor site	probably null
R6354:Phf21a	UTSW	2	92348937	missense	probably damaging	1.00
R7075:Phf21a	UTSW	2	92360379	nonsense	probably null
R7117:Phf21a	UTSW	2	92359157	missense	probably benign	0.25
R7270:Phf21a	UTSW	2	92327139	missense	probably damaging	0.98
R7708:Phf21a	UTSW	2	92327166	critical splice donor site	probably null
R7946:Phf21a	UTSW	2	92359167	missense	probably damaging	0.99
R9788:Phf21a	UTSW	2	92351633	critical splice donor site	probably null
Z1177:Phf21a	UTSW	2	92230714	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ACTTATGTGCAGCCACGGTG -3'
(R):5'- CTGTGAGGAGCAAAGGTTATGCTG -3'

Sequencing Primer
(F):5'- CCACGGTGCAAAAGGTAACATTG -3'
(R):5'- AGCAAAGGTTATGCTGTGTGCC -3'

Posted On

2019-10-24