Mutagenetix > Incidental Mutation

Incidental Mutation 'R1484:Nfya'

163356

Institutional Source

Beutler Lab

Gene Symbol

Nfya

Ensembl Gene

ENSMUSG00000023994

Gene Name

nuclear transcription factor-Y alpha

Synonyms

Sez10, Cbf-b

MMRRC Submission

039537-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1484 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

48693917-48716782 bp(-) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

A to T at 48700570 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000125034 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000046719] [ENSMUST00000078800] [ENSMUST00000159063] [ENSMUST00000159535] [ENSMUST00000160319] [ENSMUST00000162460] [ENSMUST00000161117] [ENSMUST00000161256]

AlphaFold

P23708

Predicted Effect

unknown
Transcript: ENSMUST00000046719
AA Change: V107E

SMART Domains

Protein: ENSMUSP00000043909
Gene: ENSMUSG00000023994
AA Change: V107E

Domain	Start	End	E-Value	Type
low complexity region	14	37	N/A	INTRINSIC
low complexity region	39	58	N/A	INTRINSIC
low complexity region	99	167	N/A	INTRINSIC
low complexity region	205	223	N/A	INTRINSIC
low complexity region	226	240	N/A	INTRINSIC
CBF	260	321	3.92e-35	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000078800
AA Change: V106E

SMART Domains

Protein: ENSMUSP00000077853
Gene: ENSMUSG00000023994
AA Change: V106E

Domain	Start	End	E-Value	Type
low complexity region	14	36	N/A	INTRINSIC
low complexity region	38	57	N/A	INTRINSIC
low complexity region	98	166	N/A	INTRINSIC
low complexity region	204	222	N/A	INTRINSIC
low complexity region	225	239	N/A	INTRINSIC
CBF	259	320	3.92e-35	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000159063
AA Change: V78E

SMART Domains

Protein: ENSMUSP00000124404
Gene: ENSMUSG00000023994
AA Change: V78E

Domain	Start	End	E-Value	Type
low complexity region	14	35	N/A	INTRINSIC
low complexity region	70	138	N/A	INTRINSIC
low complexity region	170	188	N/A	INTRINSIC
low complexity region	191	205	N/A	INTRINSIC
CBF	225	286	3.92e-35	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000159237

SMART Domains

Protein: ENSMUSP00000124115
Gene: ENSMUSG00000023994

Domain	Start	End	E-Value	Type
low complexity region	66	84	N/A	INTRINSIC
low complexity region	87	101	N/A	INTRINSIC
CBF	121	182	3.92e-35	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000159535
AA Change: V105E

SMART Domains

Protein: ENSMUSP00000124501
Gene: ENSMUSG00000023994
AA Change: V105E

Domain	Start	End	E-Value	Type
low complexity region	14	36	N/A	INTRINSIC
low complexity region	38	56	N/A	INTRINSIC
internal_repeat_1	57	82	3.82e-6	PROSPERO
internal_repeat_1	74	95	3.82e-6	PROSPERO
low complexity region	97	165	N/A	INTRINSIC
low complexity region	197	215	N/A	INTRINSIC
low complexity region	218	232	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000160319
AA Change: V107E

SMART Domains

Protein: ENSMUSP00000124245
Gene: ENSMUSG00000023994
AA Change: V107E

Domain	Start	End	E-Value	Type
low complexity region	14	37	N/A	INTRINSIC
low complexity region	39	58	N/A	INTRINSIC
low complexity region	99	167	N/A	INTRINSIC
low complexity region	199	217	N/A	INTRINSIC
low complexity region	220	234	N/A	INTRINSIC
CBF	254	315	3.92e-35	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160804

Predicted Effect

unknown
Transcript: ENSMUST00000162460
AA Change: V78E

SMART Domains

Protein: ENSMUSP00000123785
Gene: ENSMUSG00000023994
AA Change: V78E

Domain	Start	End	E-Value	Type
low complexity region	14	35	N/A	INTRINSIC
low complexity region	70	138	N/A	INTRINSIC
low complexity region	176	194	N/A	INTRINSIC
low complexity region	197	211	N/A	INTRINSIC
CBF	231	292	3.92e-35	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000161117
AA Change: V72E

SMART Domains

Protein: ENSMUSP00000124965
Gene: ENSMUSG00000023994
AA Change: V72E

Domain	Start	End	E-Value	Type
low complexity region	4	23	N/A	INTRINSIC
internal_repeat_1	24	49	2.33e-5	PROSPERO
internal_repeat_1	41	62	2.33e-5	PROSPERO
low complexity region	64	132	N/A	INTRINSIC
low complexity region	170	188	N/A	INTRINSIC
low complexity region	191	205	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163066

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161686

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161603

Predicted Effect

probably benign
Transcript: ENSMUST00000161256

SMART Domains

Protein: ENSMUSP00000125034
Gene: ENSMUSG00000023994

Domain	Start	End	E-Value	Type
low complexity region	1	33	N/A	INTRINSIC
low complexity region	69	87	N/A	INTRINSIC
low complexity region	90	104	N/A	INTRINSIC
CBF	124	185	9.8e-38	SMART

Meta Mutation Damage Score

0.0738

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.5%
20x: 93.4%

Validation Efficiency

97% (85/88)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is one subunit of a trimeric complex, forming a highly conserved transcription factor that binds to CCAAT motifs in the promoter regions in a variety of genes. Subunit A associates with a tight dimer composed of the B and C subunits, resulting in a trimer that binds to DNA with high specificity and affinity. The sequence specific interactions of the complex are made by the A subunit, suggesting a role as the regulatory subunit. In addition, there is evidence of post-transcriptional regulation in this gene product, either by protein degradation or control of translation. Further regulation is represented by alternative splicing in the glutamine-rich activation domain, with clear tissue-specific preferences for the two isoforms. [provided by RefSeq, Jul 2008]
PHENOTYPE: Inactivation of this locus impairs development and results in embryonic lethality. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930584F24Rik	A	T	5: 26,684,776 (GRCm39)		noncoding transcript	Het
Acvr1	A	T	2: 58,369,901 (GRCm39)	V36E	probably damaging	Het
Aldh4a1	A	G	4: 139,370,758 (GRCm39)	I414V	probably benign	Het
Alox5	C	T	6: 116,431,128 (GRCm39)	C100Y	probably damaging	Het
Ano5	T	A	7: 51,216,068 (GRCm39)	D348E	probably damaging	Het
Arhgap30	G	A	1: 171,230,839 (GRCm39)	V199M	probably damaging	Het
Arl13b	T	A	16: 62,626,999 (GRCm39)	Q234L	probably benign	Het
Atxn1	C	A	13: 45,711,052 (GRCm39)	E627*	probably null	Het
Bend3	T	C	10: 43,386,197 (GRCm39)	F197L	probably benign	Het
Brca1	A	T	11: 101,420,638 (GRCm39)	V190E	possibly damaging	Het
Brpf1	T	C	6: 113,292,096 (GRCm39)	W381R	probably damaging	Het
Brwd1	A	C	16: 95,829,491 (GRCm39)		probably null	Het
C1s2	T	C	6: 124,602,604 (GRCm39)	I530V	possibly damaging	Het
C2cd3	C	T	7: 100,089,397 (GRCm39)	R1638W	probably damaging	Het
Capns1	T	A	7: 29,893,511 (GRCm39)		probably benign	Het
Cd109	CATTTATTTATTTATTTATTTATTTATTTATTTAT	CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT	9: 78,619,782 (GRCm39)		probably benign	Het
Cep126	G	A	9: 8,100,554 (GRCm39)	T660I	possibly damaging	Het
Cep295	A	C	9: 15,246,080 (GRCm39)	I744R	probably damaging	Het
Chd3	T	C	11: 69,250,725 (GRCm39)	E668G	probably benign	Het
Chek2	A	G	5: 110,996,553 (GRCm39)	T172A	probably damaging	Het
Col6a4	A	G	9: 105,890,501 (GRCm39)		probably null	Het
Coq3	G	A	4: 21,900,291 (GRCm39)	V173I	probably benign	Het
Cyp4x1	A	T	4: 114,970,098 (GRCm39)	I343N	probably damaging	Het
Dnah7b	T	A	1: 46,176,703 (GRCm39)	D774E	probably benign	Het
Dnai3	T	C	3: 145,802,996 (GRCm39)	D65G	probably benign	Het
Ecm1	G	A	3: 95,643,275 (GRCm39)	R342C	probably damaging	Het
Esrra	T	C	19: 6,890,197 (GRCm39)	Y209C	probably damaging	Het
Gpr149	A	T	3: 62,502,592 (GRCm39)	D421E	probably benign	Het
Gpr15	T	C	16: 58,538,937 (GRCm39)	N51D	probably damaging	Het
Gpr156	T	C	16: 37,812,558 (GRCm39)	V298A	probably damaging	Het
Hmcn2	G	A	2: 31,236,507 (GRCm39)	G350D	probably damaging	Het
Ifih1	A	T	2: 62,440,902 (GRCm39)	N421K	probably benign	Het
Ilvbl	C	A	10: 78,412,564 (GRCm39)	T95K	probably damaging	Het
Itgb4	T	A	11: 115,890,625 (GRCm39)	D1104E	probably benign	Het
Katnip	C	A	7: 125,415,743 (GRCm39)		probably benign	Het
Lipf	A	T	19: 33,942,180 (GRCm39)	M37L	probably benign	Het
Lyst	T	A	13: 13,852,775 (GRCm39)	N2258K	probably benign	Het
Moxd1	A	G	10: 24,099,758 (GRCm39)	Y86C	probably damaging	Het
Muc5ac	T	C	7: 141,367,629 (GRCm39)		probably null	Het
Myo16	G	A	8: 10,610,145 (GRCm39)	R1162H	probably damaging	Het
Myo5c	A	T	9: 75,208,092 (GRCm39)	N1609Y	probably damaging	Het
Nbeal1	T	C	1: 60,240,098 (GRCm39)	F155L	probably damaging	Het
Nek4	A	T	14: 30,704,290 (GRCm39)	M602L	possibly damaging	Het
Nek9	A	G	12: 85,348,622 (GRCm39)	S971P	probably damaging	Het
Nrxn3	A	T	12: 89,221,547 (GRCm39)	N442I	probably damaging	Het
Nup42	A	C	5: 24,383,075 (GRCm39)	K200N	probably benign	Het
Or1e26	T	A	11: 73,480,187 (GRCm39)	I126L	possibly damaging	Het
Or4c111	G	A	2: 88,843,713 (GRCm39)	R232*	probably null	Het
Or7g32	G	A	9: 19,389,423 (GRCm39)	T38I	probably damaging	Het
Pcdh15	T	A	10: 74,126,833 (GRCm39)	I304N	probably damaging	Het
Pigo	G	C	4: 43,024,779 (GRCm39)	P107A	probably damaging	Het
Plce1	C	T	19: 38,693,783 (GRCm39)	Q769*	probably null	Het
Plin2	C	T	4: 86,575,481 (GRCm39)	R356H	probably benign	Het
Ppp1r9a	G	T	6: 5,113,712 (GRCm39)	E739*	probably null	Het
Ppp3cc	G	T	14: 70,478,397 (GRCm39)	N268K	probably damaging	Het
Prkag3	T	A	1: 74,779,919 (GRCm39)	D472V	probably damaging	Het
Ptch2	A	T	4: 116,968,046 (GRCm39)	D846V	probably damaging	Het
Rhob	A	T	12: 8,549,388 (GRCm39)	M82K	probably damaging	Het
Rps6kc1	T	A	1: 190,531,672 (GRCm39)	R777W	possibly damaging	Het
Sap130	T	A	18: 31,844,380 (GRCm39)	V850E	probably damaging	Het
Sema3a	T	G	5: 13,523,407 (GRCm39)	N125K	probably damaging	Het
Sema5a	A	G	15: 32,460,431 (GRCm39)	D64G	probably damaging	Het
Sgo2b	T	A	8: 64,384,507 (GRCm39)	D163V	possibly damaging	Het
Slc15a1	A	T	14: 121,728,651 (GRCm39)	Y31*	probably null	Het
Smchd1	A	T	17: 71,685,252 (GRCm39)	M1392K	probably benign	Het
Sobp	T	A	10: 43,036,827 (GRCm39)	N37I	probably damaging	Het
Spock3	G	T	8: 63,673,739 (GRCm39)	C142F	probably damaging	Het
Stx6	A	C	1: 155,053,650 (GRCm39)	S86R	probably benign	Het
Sult2a4	C	A	7: 13,643,726 (GRCm39)	M280I	probably benign	Het
Synm	A	T	7: 67,386,080 (GRCm39)	D527E	probably damaging	Het
Tax1bp1	C	T	6: 52,710,305 (GRCm39)	R195W	probably damaging	Het
Themis2	A	T	4: 132,519,796 (GRCm39)	N76K	possibly damaging	Het
Tmem8b	A	G	4: 43,690,234 (GRCm39)	T890A	probably benign	Het
Traf7	T	A	17: 24,730,785 (GRCm39)	H366L	possibly damaging	Het
Trim30c	A	T	7: 104,032,459 (GRCm39)	V289D	probably benign	Het
Tsr1	T	A	11: 74,792,914 (GRCm39)	D407E	probably damaging	Het
Ubap2	G	T	4: 41,235,593 (GRCm39)	A33E	probably damaging	Het
Unc13d	C	A	11: 115,964,701 (GRCm39)	R255L	possibly damaging	Het
Ush2a	G	T	1: 188,542,534 (GRCm39)	G3367*	probably null	Het
Vmn1r229	T	C	17: 21,034,791 (GRCm39)	L12P	probably damaging	Het
Vmn2r27	C	A	6: 124,177,474 (GRCm39)	G510V	probably damaging	Het
Vps4b	T	C	1: 106,707,712 (GRCm39)	E257G	probably damaging	Het
Vps72	T	C	3: 95,026,462 (GRCm39)	S136P	probably damaging	Het
Wdr36	T	C	18: 32,976,938 (GRCm39)	I181T	possibly damaging	Het
Wfikkn1	C	T	17: 26,096,765 (GRCm39)	A520T	probably benign	Het

Other mutations in Nfya

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02127:Nfya	APN	17	48,700,283 (GRCm39)	unclassified	probably benign
IGL02348:Nfya	APN	17	48,700,304 (GRCm39)	nonsense	probably null
IGL03220:Nfya	APN	17	48,707,521 (GRCm39)	missense	possibly damaging	0.66
IGL03274:Nfya	APN	17	48,698,375 (GRCm39)	missense	probably damaging	1.00
PIT4468001:Nfya	UTSW	17	48,702,805 (GRCm39)	missense	unknown
R0147:Nfya	UTSW	17	48,706,026 (GRCm39)	missense	possibly damaging	0.46
R0148:Nfya	UTSW	17	48,706,026 (GRCm39)	missense	possibly damaging	0.46
R0904:Nfya	UTSW	17	48,702,815 (GRCm39)	nonsense	probably null
R4105:Nfya	UTSW	17	48,699,912 (GRCm39)	nonsense	probably null
R4108:Nfya	UTSW	17	48,699,912 (GRCm39)	nonsense	probably null
R4109:Nfya	UTSW	17	48,699,912 (GRCm39)	nonsense	probably null
R4923:Nfya	UTSW	17	48,707,563 (GRCm39)	utr 5 prime	probably benign
R5411:Nfya	UTSW	17	48,699,046 (GRCm39)	missense	possibly damaging	0.83
R6299:Nfya	UTSW	17	48,699,938 (GRCm39)	intron	probably benign
R6846:Nfya	UTSW	17	48,702,715 (GRCm39)	missense	probably benign	0.04
R6967:Nfya	UTSW	17	48,699,932 (GRCm39)	intron	probably benign
R7027:Nfya	UTSW	17	48,696,340 (GRCm39)	missense	probably benign	0.00
R7634:Nfya	UTSW	17	48,699,445 (GRCm39)	missense	probably damaging	0.99
R8377:Nfya	UTSW	17	48,699,073 (GRCm39)	missense	possibly damaging	0.92
R8460:Nfya	UTSW	17	48,698,974 (GRCm39)	missense	possibly damaging	0.70
R8501:Nfya	UTSW	17	48,706,017 (GRCm39)	missense	unknown
R8726:Nfya	UTSW	17	48,699,445 (GRCm39)	missense	probably damaging	0.99
R8935:Nfya	UTSW	17	48,700,294 (GRCm39)	unclassified	probably benign
R8950:Nfya	UTSW	17	48,700,489 (GRCm39)	unclassified	probably benign
R9252:Nfya	UTSW	17	48,699,943 (GRCm39)	missense
R9321:Nfya	UTSW	17	48,707,494 (GRCm39)	missense	unknown
Z1177:Nfya	UTSW	17	48,700,541 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- ACGGAGACCCCATTTTGATGACG -3'
(R):5'- GCCTTTGCTGCCATCAGCATAAC -3'

Sequencing Primer
(F):5'- TCACATCCCATGTGAACCAGG -3'
(R):5'- cctaataaccctacctctgcc -3'

Posted On

2014-03-28