Mutagenetix > Incidental Mutation

Incidental Mutation 'R7027:Nfya'

546084

Institutional Source

Beutler Lab

Gene Symbol

Nfya

Ensembl Gene

ENSMUSG00000023994

Gene Name

nuclear transcription factor-Y alpha

Synonyms

Sez10, Cbf-b

MMRRC Submission

045128-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7027 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

48693917-48716782 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 48696340 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 335 (T335A)

Ref Sequence

ENSEMBL: ENSMUSP00000124245 (fasta)

Gene Model

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

AlphaFold

P23708

Predicted Effect

probably benign
Transcript: ENSMUST00000046719
AA Change: T341A

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

SMART Domains

Protein: ENSMUSP00000043909
Gene: ENSMUSG00000023994
AA Change: T341A

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

probably benign
Transcript: ENSMUST00000078800
AA Change: T340A

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

SMART Domains

Protein: ENSMUSP00000077853
Gene: ENSMUSG00000023994
AA Change: T340A

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: T306A

SMART Domains

Protein: ENSMUSP00000124404
Gene: ENSMUSG00000023994
AA Change: T306A

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

SMART Domains

Protein: ENSMUSP00000124115
Gene: ENSMUSG00000023994
AA Change: T201A

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

probably benign
Transcript: ENSMUST00000159535

SMART Domains

Protein: ENSMUSP00000124501
Gene: ENSMUSG00000023994

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

probably benign
Transcript: ENSMUST00000160319
AA Change: T335A

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

SMART Domains

Protein: ENSMUSP00000124245
Gene: ENSMUSG00000023994
AA Change: T335A

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

probably benign
Transcript: ENSMUST00000161117

SMART Domains

Protein: ENSMUSP00000124965
Gene: ENSMUSG00000023994

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

probably benign
Transcript: ENSMUST00000161256
AA Change: T205A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000125034
Gene: ENSMUSG00000023994
AA Change: T205A

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

Predicted Effect

unknown
Transcript: ENSMUST00000162460
AA Change: T312A

SMART Domains

Protein: ENSMUSP00000123785
Gene: ENSMUSG00000023994
AA Change: T312A

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

98% (85/87)

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acoxl	A	T	2: 127,852,003 (GRCm39)	M102L	probably benign	Het
Adcy10	A	G	1: 165,345,815 (GRCm39)	E288G	probably damaging	Het
Agap1	A	G	1: 89,816,444 (GRCm39)	H748R	probably benign	Het
Ahsg	T	C	16: 22,711,007 (GRCm39)	L48P	probably damaging	Het
Ankrd27	A	G	7: 35,311,951 (GRCm39)	T394A	probably benign	Het
Apc	T	G	18: 34,445,129 (GRCm39)	V657G	probably damaging	Het
Arl2	T	C	19: 6,191,119 (GRCm39)	T5A	probably benign	Het
B020011L13Rik	A	G	1: 117,729,180 (GRCm39)	Y229C	probably benign	Het
B3gnt5	T	A	16: 19,588,740 (GRCm39)	S320T	probably damaging	Het
Bach1	G	A	16: 87,516,179 (GRCm39)	R240Q	probably benign	Het
BC107364	T	G	3: 96,348,057 (GRCm39)	R77S	unknown	Het
Brox	G	A	1: 183,065,750 (GRCm39)	P206L	possibly damaging	Het
Ccrl2	T	C	9: 110,884,953 (GRCm39)	K182E	probably benign	Het
Cd19	A	G	7: 126,009,671 (GRCm39)	V465A	possibly damaging	Het
Chrdl2	A	T	7: 99,671,240 (GRCm39)	Q126H	probably damaging	Het
Cnbd1	G	A	4: 18,862,063 (GRCm39)	P376S	probably benign	Het
Cobll1	A	G	2: 64,919,847 (GRCm39)	S1194P	probably benign	Het
Col6a4	T	C	9: 105,944,213 (GRCm39)	Y1087C	probably damaging	Het
Col9a2	G	A	4: 120,901,216 (GRCm39)		probably null	Het
Cyp4v3	A	G	8: 45,763,289 (GRCm39)	S341P	possibly damaging	Het
Dnah7a	T	A	1: 53,670,665 (GRCm39)	Y529F	probably benign	Het
Eif3b	C	T	5: 140,411,043 (GRCm39)	R165W	probably damaging	Het
Erlec1	C	A	11: 30,900,790 (GRCm39)	C126F	probably damaging	Het
Fads2b	A	G	2: 85,315,871 (GRCm39)	Y440H	probably damaging	Het
Fat2	T	C	11: 55,160,259 (GRCm39)	T3285A	probably benign	Het
Fat2	G	A	11: 55,172,677 (GRCm39)	R2679*	probably null	Het
Fbxo31	T	C	8: 122,305,224 (GRCm39)	T91A	probably damaging	Het
Fkbp5	A	G	17: 28,631,037 (GRCm39)	Y243H	probably damaging	Het
Flcn	C	T	11: 59,686,632 (GRCm39)	V374M	probably damaging	Het
Fndc5	A	G	4: 129,033,316 (GRCm39)	M128V	probably benign	Het
Gal3st1	A	G	11: 3,949,002 (GRCm39)	D403G	probably damaging	Het
Garem1	T	C	18: 21,263,051 (GRCm39)	N588D	probably benign	Het
Gas1	T	C	13: 60,324,047 (GRCm39)	T196A	probably damaging	Het
Gcn1	T	C	5: 115,754,605 (GRCm39)		probably null	Het
Gprc5d	T	G	6: 135,093,646 (GRCm39)	Q87P	probably damaging	Het
Grm1	A	G	10: 10,595,339 (GRCm39)	L763P	probably damaging	Het
Hivep2	G	T	10: 14,025,321 (GRCm39)	K2378N	probably damaging	Het
Hivep2	G	T	10: 14,025,322 (GRCm39)	D2379Y	probably damaging	Het
Itgad	A	G	7: 127,782,161 (GRCm39)	Y199C	probably damaging	Het
Itm2c	A	G	1: 85,834,206 (GRCm39)	I174V	probably benign	Het
Khdrbs2	A	G	1: 32,453,997 (GRCm39)	S128G	probably benign	Het
Map3k9	T	C	12: 81,777,398 (GRCm39)	T528A	probably benign	Het
Mmp11	G	A	10: 75,768,230 (GRCm39)		probably benign	Het
Mycbpap	T	A	11: 94,405,440 (GRCm39)	I30F	probably damaging	Het
Npat	T	A	9: 53,481,216 (GRCm39)	S1008T	possibly damaging	Het
Or10al5	G	A	17: 38,063,300 (GRCm39)	C185Y	probably damaging	Het
Or12e10	A	G	2: 87,641,060 (GRCm39)	T299A	possibly damaging	Het
Or5p69	A	T	7: 107,967,557 (GRCm39)	M287L	probably damaging	Het
Or6c219	C	T	10: 129,781,041 (GRCm39)	A297T	possibly damaging	Het
Osbpl10	T	C	9: 115,052,766 (GRCm39)	V613A	probably damaging	Het
Pcdhga8	T	C	18: 37,860,164 (GRCm39)	W407R	probably benign	Het
Pcdhgb4	A	G	18: 37,854,415 (GRCm39)	D270G	probably damaging	Het
Pde2a	A	C	7: 101,160,804 (GRCm39)	E918D	probably damaging	Het
Plekhg5	A	G	4: 152,198,431 (GRCm39)	D873G	probably benign	Het
Pno1	A	T	11: 17,158,880 (GRCm39)	S173T	possibly damaging	Het
Ppfia3	A	G	7: 45,004,160 (GRCm39)	I494T	possibly damaging	Het
Prkrip1	C	A	5: 136,210,267 (GRCm39)		probably benign	Het
Psma5	A	G	3: 108,172,484 (GRCm39)	I67V	probably benign	Het
Reep6	G	A	10: 80,169,799 (GRCm39)		probably null	Het
Rtl1	CTCTTCTTCTTCACCATCTTCCTCCTCCTCCCCTTCTTCTTCTTCACCATCTTCCTCCTCCTCCCCTTCTTCTTCTTCACCATCTTCCTCCTCCTC	CTCTTCTTCTTCACCATCTTCCTCCTCCTCCCCTTCTTCTTCTTCACCATCTTCCTCCTCCTC	12: 109,557,848 (GRCm39)		probably benign	Het
Scyl2	C	G	10: 89,481,323 (GRCm39)		probably null	Het
Sdk1	T	A	5: 142,082,481 (GRCm39)		probably null	Het
Senp5	C	A	16: 31,808,113 (GRCm39)	K380N	probably benign	Het
Slc22a14	A	T	9: 119,060,281 (GRCm39)		probably null	Het
Slc26a5	T	A	5: 22,021,972 (GRCm39)	T485S	possibly damaging	Het
Slc44a5	T	C	3: 153,959,356 (GRCm39)	I349T	probably benign	Het
Smarca5	T	C	8: 81,463,355 (GRCm39)	E71G	probably benign	Het
Smok2a	A	T	17: 13,444,666 (GRCm39)	H81L	probably damaging	Het
Snrnp200	A	G	2: 127,059,192 (GRCm39)	D388G	probably benign	Het
Tank	T	C	2: 61,483,766 (GRCm39)	V404A	probably benign	Het
Tek	A	G	4: 94,753,747 (GRCm39)	D1063G	probably damaging	Het
Tfap2a	C	T	13: 40,887,150 (GRCm39)	C16Y	probably benign	Het
Tmc1	A	G	19: 20,918,267 (GRCm39)		probably null	Het
Tnc	A	G	4: 63,902,826 (GRCm39)	F1484L	probably benign	Het
Tnfsf13	T	A	11: 69,575,958 (GRCm39)		probably null	Het
Tnrc6c	T	A	11: 117,624,444 (GRCm39)	S919T	probably damaging	Het
Trim17	C	A	11: 58,859,442 (GRCm39)	Q219K	probably benign	Het
Trim5	T	A	7: 103,914,875 (GRCm39)	H389L	probably benign	Het
Trio	T	A	15: 27,805,740 (GRCm39)	M583L	possibly damaging	Het
Ttll10	A	T	4: 156,120,258 (GRCm39)	H389Q	possibly damaging	Het
Usp24	T	C	4: 106,219,441 (GRCm39)	S546P	probably benign	Het
Vmn1r19	T	A	6: 57,381,475 (GRCm39)	Y9*	probably null	Het
Vmn2r50	T	A	7: 9,781,539 (GRCm39)	D402V	probably damaging	Het
Vmn2r93	C	A	17: 18,533,548 (GRCm39)	A484E	probably benign	Het
Vps13a	T	C	19: 16,642,028 (GRCm39)	T2200A	probably benign	Het
Wdr36	T	A	18: 32,974,958 (GRCm39)	H103Q	probably benign	Het
Zfp534	G	A	4: 147,759,667 (GRCm39)	T334I	possibly damaging	Het
Zfp804b	C	T	5: 6,820,372 (GRCm39)	S897N	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
R1484:Nfya	UTSW	17	48,700,570 (GRCm39)	unclassified	probably benign
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
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'- TGTCAGCCATCATTGCAGCTG -3'
(R):5'- TAGGAACTGCCAGCTGTAGG -3'

Sequencing Primer
(F):5'- CCATCATTGCAGCTGTAATACTGAGC -3'
(R):5'- ATGCTGACATGGGAAGTTCC -3'

Posted On

2019-05-13