Mutagenetix > Incidental Mutation

Incidental Mutation 'R5055:Phf21a'

390748

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

042645-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5055 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

92014096-92195011 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 92182201 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 377 (S377P)

Ref Sequence

ENSEMBL: ENSMUSP00000123955 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000044036] [ENSMUST00000068702] [ENSMUST00000090586] [ENSMUST00000111290] [ENSMUST00000111291] [ENSMUST00000111292] [ENSMUST00000111293] [ENSMUST00000159961] [ENSMUST00000111294] [ENSMUST00000111297]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000044036
AA Change: S406P

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000038497
Gene: ENSMUSG00000058318
AA Change: S406P

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: S490P

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

SMART Domains

Protein: ENSMUSP00000088074
Gene: ENSMUSG00000058318
AA Change: S490P

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 damaging
Transcript: ENSMUST00000111290
AA Change: S461P

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000106921
Gene: ENSMUSG00000058318
AA Change: S461P

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: S406P

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000106922
Gene: ENSMUSG00000058318
AA Change: S406P

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 damaging
Transcript: ENSMUST00000111293
AA Change: S490P

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

SMART Domains

Protein: ENSMUSP00000106924
Gene: ENSMUSG00000058318
AA Change: S490P

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 damaging
Transcript: ENSMUST00000159961
AA Change: S377P

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

SMART Domains

Protein: ENSMUSP00000123955
Gene: ENSMUSG00000058318
AA Change: S377P

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: 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

0.0758

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.5%
20x: 92.9%

Validation Efficiency

98% (84/86)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam19	G	A	11: 46,013,996 (GRCm39)	V329I	probably damaging	Het
Adgrl3	C	A	5: 81,794,398 (GRCm39)	A541E	possibly damaging	Het
Agbl1	A	T	7: 76,063,325 (GRCm39)	I263F	probably damaging	Het
Ash1l	T	C	3: 88,930,519 (GRCm39)		probably null	Het
Bccip	A	G	7: 133,316,652 (GRCm39)	T91A	probably benign	Het
Bnc1	A	T	7: 81,624,163 (GRCm39)	F355I	probably damaging	Het
Bpifa2	A	T	2: 153,855,630 (GRCm39)	D185V	probably damaging	Het
Capn8	T	A	1: 182,399,526 (GRCm39)	V89D	probably damaging	Het
Cfap46	A	T	7: 139,241,106 (GRCm39)	M421K	probably damaging	Het
Chd2	A	T	7: 73,130,256 (GRCm39)	L800M	probably damaging	Het
Chd4	A	G	6: 125,077,949 (GRCm39)	D137G	possibly damaging	Het
Crtap	A	G	9: 114,219,208 (GRCm39)	Y154H	probably benign	Het
Ctdp1	T	A	18: 80,499,303 (GRCm39)	Q213L	probably damaging	Het
Cts6	T	C	13: 61,344,164 (GRCm39)	Y296C	probably damaging	Het
Daxx	G	T	17: 34,131,134 (GRCm39)	V354F	probably benign	Het
Dnah2	A	G	11: 69,411,599 (GRCm39)	I341T	possibly damaging	Het
Epha2	A	G	4: 141,036,380 (GRCm39)	D272G	probably benign	Het
Etfa	A	G	9: 55,407,417 (GRCm39)	V24A	probably damaging	Het
Fbxl7	C	A	15: 26,553,022 (GRCm39)	G82W	probably damaging	Het
Fcamr	G	A	1: 130,739,174 (GRCm39)	C158Y	probably damaging	Het
Fyb1	A	C	15: 6,614,630 (GRCm39)		probably benign	Het
Gars1	G	A	6: 55,045,077 (GRCm39)	R454H	probably damaging	Het
Ghsr	T	C	3: 27,426,421 (GRCm39)	V159A	probably benign	Het
Glp1r	A	T	17: 31,137,861 (GRCm39)	Q97H	probably benign	Het
Gm27047	T	C	6: 130,606,909 (GRCm39)		noncoding transcript	Het
Igkv3-3	A	C	6: 70,664,223 (GRCm39)	I22L	probably benign	Het
Inpp5b	G	T	4: 124,636,824 (GRCm39)		probably null	Het
Ipo9	C	A	1: 135,330,097 (GRCm39)	E448*	probably null	Het
Itgb2l	A	T	16: 96,229,003 (GRCm39)	I400N	probably damaging	Het
Kat6b	T	A	14: 21,567,062 (GRCm39)	H40Q	probably damaging	Het
Kcna7	G	A	7: 45,056,015 (GRCm39)	R77H	probably damaging	Het
Kcnq2	G	T	2: 180,728,554 (GRCm39)		probably benign	Het
Klf7	T	C	1: 64,118,439 (GRCm39)	T53A	probably benign	Het
Kmt2a	A	G	9: 44,729,649 (GRCm39)		probably benign	Het
Lrp10	C	T	14: 54,705,802 (GRCm39)	R331C	probably benign	Het
Map4k5	A	T	12: 69,878,332 (GRCm39)	D289E	probably benign	Het
Mfsd4b2	A	T	10: 39,799,773 (GRCm39)	M43K	possibly damaging	Het
Msr1	T	G	8: 40,076,997 (GRCm39)	R138S	possibly damaging	Het
Myh7b	G	C	2: 155,474,293 (GRCm39)	R1669S	possibly damaging	Het
Myh9	G	A	15: 77,648,723 (GRCm39)	A1711V	probably benign	Het
Myo18b	A	G	5: 113,023,083 (GRCm39)		probably benign	Het
Nampt	A	T	12: 32,883,120 (GRCm39)	N102Y	possibly damaging	Het
Nell2	T	C	15: 95,371,460 (GRCm39)	I92V	probably benign	Het
Nes	A	G	3: 87,884,521 (GRCm39)	N883D	probably benign	Het
Neurl3	T	A	1: 36,312,463 (GRCm39)		probably benign	Het
Ocln	T	A	13: 100,675,930 (GRCm39)	T188S	probably benign	Het
Or2ag20	T	A	7: 106,464,937 (GRCm39)	M250K	probably damaging	Het
Or5m10	T	C	2: 85,717,585 (GRCm39)	F147S	probably benign	Het
Parp14	T	A	16: 35,664,733 (GRCm39)	Q1305L	probably benign	Het
Pde3a	C	T	6: 141,433,682 (GRCm39)	Q855*	probably null	Het
Pde4b	T	C	4: 102,052,311 (GRCm39)		probably benign	Het
Pdk2	T	C	11: 94,930,242 (GRCm39)	M65V	probably benign	Het
Plcb2	T	A	2: 118,548,703 (GRCm39)	T408S	probably benign	Het
Ppp1r12b	G	T	1: 134,883,471 (GRCm39)	A17E	probably benign	Het
Ppp6r2	A	G	15: 89,167,152 (GRCm39)	D789G	probably benign	Het
Prdm16	T	C	4: 154,419,719 (GRCm39)	M897V	possibly damaging	Het
Prss57	A	G	10: 79,620,178 (GRCm39)		probably null	Het
Psd	G	T	19: 46,310,907 (GRCm39)	L381I	probably benign	Het
Ptprq	A	T	10: 107,370,540 (GRCm39)	D2050E	probably benign	Het
Rfc1	G	T	5: 65,423,505 (GRCm39)	N1034K	probably damaging	Het
Ryr3	C	T	2: 112,661,504 (GRCm39)	G1829S	probably benign	Het
Scaper	T	C	9: 55,767,003 (GRCm39)		probably null	Het
Scn5a	A	G	9: 119,351,632 (GRCm39)	I783T	probably damaging	Het
Slc28a1	A	G	7: 80,818,796 (GRCm39)	N583S	possibly damaging	Het
Slc35e3	C	T	10: 117,580,884 (GRCm39)	G140D	probably damaging	Het
Slc6a9	G	A	4: 117,725,347 (GRCm39)		probably null	Het
Sptlc1	A	G	13: 53,496,218 (GRCm39)	S376P	probably benign	Het
Sspo	G	A	6: 48,441,729 (GRCm39)	C1913Y	probably damaging	Het
Taar7b	A	T	10: 23,876,845 (GRCm39)	I337F	possibly damaging	Het
Tdpoz2	T	A	3: 93,559,235 (GRCm39)	I246F	probably damaging	Het
Trpa1	C	T	1: 14,946,183 (GRCm39)	V983M	probably damaging	Het
Trpm5	A	T	7: 142,626,521 (GRCm39)	M1112K	probably benign	Het
Tsbp1	G	A	17: 34,667,770 (GRCm39)	C154Y	possibly damaging	Het
Uso1	A	T	5: 92,340,594 (GRCm39)	K670I	probably benign	Het
Washc4	A	G	10: 83,392,771 (GRCm39)	D257G	probably damaging	Het
Wdr41	T	A	13: 95,151,725 (GRCm39)		probably null	Het
Zbtb17	A	G	4: 141,193,860 (GRCm39)	Q668R	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
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'- ACACTGGCCAAAGGTATGTAAG -3'
(R):5'- CCCCATAAGAAAGCTGCCTG -3'

Sequencing Primer
(F):5'- GGTATGTAAGATCATTTTCCCCTG -3'
(R):5'- AGCTGCCTGGCAAGGTATG -3'

Posted On

2016-06-06