Mutagenetix > Incidental Mutation

Incidental Mutation 'R7075:Phf21a'

549145

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

045170-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7075 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

92014096-92195011 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

C to T at 92190724 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Stop codon at position 675 (Q675*)

Ref Sequence

ENSEMBL: ENSMUSP00000088074 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000044036] [ENSMUST00000068586] [ENSMUST00000068702] [ENSMUST00000090582] [ENSMUST00000090586] [ENSMUST00000111284] [ENSMUST00000111290] [ENSMUST00000111291] [ENSMUST00000111292] [ENSMUST00000111293] [ENSMUST00000111294] [ENSMUST00000111297] [ENSMUST00000148352] [ENSMUST00000159961] [ENSMUST00000176289] [ENSMUST00000176774] [ENSMUST00000176810]

AlphaFold

no structure available at present

Predicted Effect

probably null
Transcript: ENSMUST00000044036
AA Change: Q591*

SMART Domains

Protein: ENSMUSP00000038497
Gene: ENSMUSG00000058318
AA Change: Q591*

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: ENSMUST00000068586

SMART Domains

Protein: ENSMUSP00000064128
Gene: ENSMUSG00000040434

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
low complexity region	52	63	N/A	INTRINSIC
Pfam:Glyco_transf_8	70	316	4.6e-22	PFAM
low complexity region	392	401	N/A	INTRINSIC
Pfam:Glyco_transf_49	402	469	2.2e-11	PFAM
Pfam:Glyco_transf_49	466	673	1e-42	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000068702
AA Change: Q543*

SMART Domains

Protein: ENSMUSP00000070649
Gene: ENSMUSG00000058318
AA Change: Q543*

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: ENSMUST00000090582

SMART Domains

Protein: ENSMUSP00000088070
Gene: ENSMUSG00000040434

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
low complexity region	52	63	N/A	INTRINSIC
Pfam:Glyco_transf_8	70	218	7.2e-9	PFAM
Pfam:Glyco_transf_8	188	281	2.3e-8	PFAM
low complexity region	357	366	N/A	INTRINSIC
Pfam:Glyco_transf_49	367	434	2.1e-11	PFAM
Pfam:Glyco_transf_49	431	638	9.3e-43	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000090586
AA Change: Q675*

SMART Domains

Protein: ENSMUSP00000088074
Gene: ENSMUSG00000058318
AA Change: Q675*

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: ENSMUST00000111284

SMART Domains

Protein: ENSMUSP00000106915
Gene: ENSMUSG00000040434

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
low complexity region	77	88	N/A	INTRINSIC
Pfam:Glyco_transf_8	97	341	8.9e-22	PFAM
low complexity region	417	426	N/A	INTRINSIC
Pfam:Glyco_transf_49	427	494	6.5e-11	PFAM
Pfam:Glyco_transf_49	491	698	3.1e-42	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000111290
AA Change: Q646*

SMART Domains

Protein: ENSMUSP00000106921
Gene: ENSMUSG00000058318
AA Change: Q646*

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 null
Transcript: ENSMUST00000111291
AA Change: Q591*

SMART Domains

Protein: ENSMUSP00000106922
Gene: ENSMUSG00000058318
AA Change: Q591*

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 null
Transcript: ENSMUST00000111292
AA Change: Q543*

SMART Domains

Protein: ENSMUSP00000106923
Gene: ENSMUSG00000058318
AA Change: Q543*

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 null
Transcript: ENSMUST00000111293
AA Change: Q675*

SMART Domains

Protein: ENSMUSP00000106924
Gene: ENSMUSG00000058318
AA Change: Q675*

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 null
Transcript: ENSMUST00000111294
AA Change: Q628*

SMART Domains

Protein: ENSMUSP00000106925
Gene: ENSMUSG00000058318
AA Change: Q628*

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 null
Transcript: ENSMUST00000111297
AA Change: Q598*

SMART Domains

Protein: ENSMUSP00000106928
Gene: ENSMUSG00000058318
AA Change: Q598*

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: ENSMUST00000148352

SMART Domains

Protein: ENSMUSP00000135451
Gene: ENSMUSG00000040434

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
low complexity region	52	63	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000159961
AA Change: Q562*

SMART Domains

Protein: ENSMUSP00000123955
Gene: ENSMUSG00000058318
AA Change: Q562*

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: ENSMUST00000176289

SMART Domains

Protein: ENSMUSP00000135118
Gene: ENSMUSG00000040434

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
low complexity region	52	63	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000176774

SMART Domains

Protein: ENSMUSP00000135400
Gene: ENSMUSG00000040434

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
low complexity region	52	63	N/A	INTRINSIC
Pfam:Glyco_transf_8	71	317	3.9e-22	PFAM
low complexity region	393	402	N/A	INTRINSIC
Pfam:Glyco_transf_49	403	470	1.6e-11	PFAM
Pfam:Glyco_transf_49	467	674	7.4e-43	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000176810

SMART Domains

Protein: ENSMUSP00000135024
Gene: ENSMUSG00000040434

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
low complexity region	77	88	N/A	INTRINSIC
Pfam:Glyco_transf_8	101	342	4.2e-20	PFAM
low complexity region	417	426	N/A	INTRINSIC
Pfam:Glyco_transf_49	427	493	1.3e-13	PFAM
Pfam:Glyco_transf_49	489	698	2.8e-46	PFAM

Coding Region Coverage

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

Validation Efficiency

95% (60/63)

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: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acyp1	A	T	12: 85,325,782 (GRCm39)	H72Q	unknown	Het
Afmid	T	A	11: 117,726,531 (GRCm39)	D218E	probably benign	Het
Ankhd1	T	C	18: 36,693,042 (GRCm39)	V1A		Het
Atf7ip	T	C	6: 136,573,513 (GRCm39)		probably null	Het
BC024139	C	T	15: 76,008,599 (GRCm39)	V326I	probably benign	Het
Bfsp1	T	A	2: 143,690,885 (GRCm39)	Q159L	probably damaging	Het
Cct2	A	T	10: 116,897,370 (GRCm39)	W125R	unknown	Het
Cnksr3	G	T	10: 7,102,931 (GRCm39)	T147K	probably benign	Het
Colq	C	G	14: 31,274,866 (GRCm39)	G101R	probably damaging	Het
Dlg5	G	T	14: 24,227,865 (GRCm39)	T352K	possibly damaging	Het
Dusp9	TAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAG	TAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAG	X: 72,684,217 (GRCm39)		probably benign	Het
Ebna1bp2	T	C	4: 118,479,299 (GRCm39)	V119A	probably benign	Het
Eif2ak4	C	T	2: 118,251,291 (GRCm39)	Q318*	probably null	Het
Eif2b1	G	A	5: 124,709,314 (GRCm39)	T286M	probably damaging	Het
Fam53b	G	T	7: 132,361,352 (GRCm39)	D225E	probably damaging	Het
Fh1	A	G	1: 175,435,421 (GRCm39)	I354T	probably benign	Het
Fnbp1	T	C	2: 30,948,926 (GRCm39)	H206R	probably benign	Het
Gabrg3	A	T	7: 56,973,444 (GRCm39)	D74E	probably damaging	Het
Galnt18	A	T	7: 111,155,595 (GRCm39)	V246E	possibly damaging	Het
Glt6d1	T	C	2: 25,685,292 (GRCm39)	R44G	probably benign	Het
Gm17087	T	C	17: 8,785,635 (GRCm39)	M23V	probably benign	Het
Gpr160	A	T	3: 30,950,926 (GRCm39)	I333L	possibly damaging	Het
Hars1	T	C	18: 36,905,408 (GRCm39)	N142S	possibly damaging	Het
Hmgcll1	T	C	9: 75,963,834 (GRCm39)	V97A	possibly damaging	Het
Itih4	T	G	14: 30,614,560 (GRCm39)	V474G	probably damaging	Het
Itprid2	T	A	2: 79,466,004 (GRCm39)	S41T	probably damaging	Het
Keap1	C	T	9: 21,142,552 (GRCm39)	V568I	probably benign	Het
Kifc5b	A	G	17: 27,144,872 (GRCm39)	M633V	probably benign	Het
Lsm4	A	G	8: 71,130,435 (GRCm39)	E18G	probably damaging	Het
Meox1	T	A	11: 101,784,569 (GRCm39)	Q88L	probably damaging	Het
Mettl25	T	C	10: 105,665,785 (GRCm39)	N147S	possibly damaging	Het
Mphosph9	A	C	5: 124,458,922 (GRCm39)	W83G	probably damaging	Het
Or1j15	T	C	2: 36,459,192 (GRCm39)	I194T	probably benign	Het
Or5ak22	T	C	2: 85,230,544 (GRCm39)	D111G	probably damaging	Het
Or7e170	T	A	9: 19,795,359 (GRCm39)	M81L	probably benign	Het
Or8b4	T	C	9: 37,830,370 (GRCm39)	V139A	probably benign	Het
Or8h8	T	G	2: 86,752,990 (GRCm39)	K295N	possibly damaging	Het
Or9g4	T	A	2: 85,505,168 (GRCm39)	Y109F		Het
Otogl	G	T	10: 107,614,790 (GRCm39)	T1954K	probably benign	Het
Padi2	T	C	4: 140,660,528 (GRCm39)	V336A	probably damaging	Het
Ppip5k1	T	C	2: 121,152,231 (GRCm39)	E1092G	probably damaging	Het
Psg21	T	C	7: 18,388,786 (GRCm39)	N102S	probably damaging	Het
Ralgapa1	C	A	12: 55,867,508 (GRCm39)	Q15H	possibly damaging	Het
Rbm26	A	T	14: 105,398,043 (GRCm39)	D26E	unknown	Het
Rbp4	T	C	19: 38,112,509 (GRCm39)	Y152C	probably damaging	Het
Recql4	A	G	15: 76,590,624 (GRCm39)	V646A	possibly damaging	Het
Rnf220	A	T	4: 117,143,079 (GRCm39)	M63K	probably benign	Het
Selenok	T	C	14: 29,692,024 (GRCm39)	S21P	probably damaging	Het
Senp1	A	G	15: 97,956,207 (GRCm39)	V404A	probably benign	Het
Sh3yl1	A	G	12: 30,990,165 (GRCm39)		probably null	Het
Snx32	A	G	19: 5,547,018 (GRCm39)	L275P	probably damaging	Het
Stat5a	T	C	11: 100,770,519 (GRCm39)	V519A	possibly damaging	Het
Tbc1d10b	A	T	7: 126,802,410 (GRCm39)	V388E	possibly damaging	Het
Tdrd6	A	G	17: 43,936,065 (GRCm39)	V1661A	probably benign	Het
Tmem63a	T	A	1: 180,788,714 (GRCm39)	F350L	probably damaging	Het
Trio	A	T	15: 27,898,086 (GRCm39)	I401K	unknown	Het
Ttn	T	C	2: 76,547,173 (GRCm39)	E32291G	probably damaging	Het
Tubgcp5	G	T	7: 55,479,155 (GRCm39)	V1002L	probably benign	Het
Vav3	C	T	3: 109,433,240 (GRCm39)	T410I	possibly damaging	Het
Vmn1r1	A	T	1: 181,985,597 (GRCm39)	F23I	probably benign	Het
Vmn2r84	T	A	10: 130,226,941 (GRCm39)	Q299L	probably damaging	Het
Vmn2r85	T	A	10: 130,258,557 (GRCm39)	E499D	probably benign	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
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
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'- CGTTTGCTGCAGAAATGTATGG -3'
(R):5'- TGGCACAAGCATCTTCTCTC -3'

Sequencing Primer
(F):5'- TGAAGAGCAGCATCCTGGC -3'
(R):5'- TTCTCTCTCTCTGGAACCAAAGAAC -3'

Posted On

2019-05-15