Mutagenetix > Incidental Mutation

Incidental Mutation 'R0148:Nfya'

60890

Institutional Source

Beutler Lab

Gene Symbol

Nfya

Ensembl Gene

ENSMUSG00000023994

Gene Name

nuclear transcription factor-Y alpha

Synonyms

Sez10, Cbf-b

MMRRC Submission

038432-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0148 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

48693917-48716782 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 48706026 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 48 (V48A)

Ref Sequence

ENSEMBL: ENSMUSP00000124501 (fasta)

Gene Model

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

AlphaFold

P23708

Predicted Effect

unknown
Transcript: ENSMUST00000046719
AA Change: V49A

SMART Domains

Protein: ENSMUSP00000043909
Gene: ENSMUSG00000023994
AA Change: V49A

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: V48A

SMART Domains

Protein: ENSMUSP00000077853
Gene: ENSMUSG00000023994
AA Change: V48A

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

probably benign
Transcript: ENSMUST00000159063

SMART Domains

Protein: ENSMUSP00000124404
Gene: ENSMUSG00000023994

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

possibly damaging
Transcript: ENSMUST00000159535
AA Change: V48A

PolyPhen 2 Score 0.455 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000124501
Gene: ENSMUSG00000023994
AA Change: V48A

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: V49A

SMART Domains

Protein: ENSMUSP00000124245
Gene: ENSMUSG00000023994
AA Change: V49A

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: ENSMUST00000161117
AA Change: V14A

SMART Domains

Protein: ENSMUSP00000124965
Gene: ENSMUSG00000023994
AA Change: V14A

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: ENSMUST00000161686

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163066

Predicted Effect

probably benign
Transcript: ENSMUST00000162460

SMART Domains

Protein: ENSMUSP00000123785
Gene: ENSMUSG00000023994

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

Meta Mutation Damage Score

0.0725

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 96.0%
20x: 91.8%

Validation Efficiency

86% (30/35)

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2m	T	C	6: 121,639,405 (GRCm39)		probably null	Het
Agtr1a	T	C	13: 30,565,927 (GRCm39)	S331P	probably benign	Het
Ank1	T	A	8: 23,613,993 (GRCm39)	N1545K	probably damaging	Het
Bahcc1	A	T	11: 120,159,230 (GRCm39)	Q152H	probably damaging	Het
Bend3	T	A	10: 43,387,946 (GRCm39)	Y780N	probably damaging	Het
Bod1l	G	T	5: 41,976,040 (GRCm39)	A1758E	possibly damaging	Het
Ctcfl	T	C	2: 172,960,340 (GRCm39)	D81G	possibly damaging	Het
Ddx39a	C	T	8: 84,449,105 (GRCm39)	R298C	possibly damaging	Het
Dock8	T	C	19: 25,096,823 (GRCm39)	L577P	probably benign	Het
Drc1	A	T	5: 30,486,487 (GRCm39)	N13I	possibly damaging	Het
Efl1	T	C	7: 82,320,878 (GRCm39)	S104P	probably damaging	Het
Eml4	T	A	17: 83,729,081 (GRCm39)	N85K	probably damaging	Het
Epb41l4a	T	C	18: 33,931,853 (GRCm39)	T581A	probably damaging	Het
Epha3	T	C	16: 63,433,307 (GRCm39)	D446G	possibly damaging	Het
Fam209	G	T	2: 172,315,900 (GRCm39)	G92C	probably damaging	Het
Fbln1	G	A	15: 85,115,027 (GRCm39)	R193H	probably damaging	Het
Fbxw21	A	G	9: 108,977,085 (GRCm39)		probably null	Het
Fgf17	C	T	14: 70,876,313 (GRCm39)	R49Q	probably damaging	Het
Flnb	T	C	14: 7,939,077 (GRCm38)	S2307P	probably benign	Het
Galr1	A	G	18: 82,423,695 (GRCm39)	L194P	probably benign	Het
Gar1	T	C	3: 129,623,122 (GRCm39)	H89R	probably damaging	Het
Gbp4	T	A	5: 105,267,362 (GRCm39)	Y519F	probably benign	Het
Git1	A	G	11: 77,396,554 (GRCm39)	T601A	probably benign	Het
Gm10722	T	"C,A"	9: 3,001,405 (GRCm39)		probably null	Het
Gm5142	C	T	14: 59,416,119 (GRCm39)	R13H	possibly damaging	Het
Gria2	A	C	3: 80,615,038 (GRCm39)	W481G	probably damaging	Het
Homer2	T	C	7: 81,274,026 (GRCm39)	T57A	probably benign	Het
Hpse2	A	C	19: 42,920,099 (GRCm39)		probably null	Het
Hspb7	T	C	4: 141,151,302 (GRCm39)	I148T	probably damaging	Het
Htr1d	C	A	4: 136,170,788 (GRCm39)	T339K	probably damaging	Het
Il4ra	T	A	7: 125,174,709 (GRCm39)	C306S	probably damaging	Het
Kansl3	A	T	1: 36,392,897 (GRCm39)	C225S	probably damaging	Het
Lama3	G	A	18: 12,581,329 (GRCm39)	C596Y	probably damaging	Het
Lama5	T	C	2: 179,832,199 (GRCm39)	H1714R	probably benign	Het
Marchf6	C	T	15: 31,490,758 (GRCm39)	V293M	probably damaging	Het
Med12l	A	G	3: 58,945,075 (GRCm39)	D100G	probably damaging	Het
Mettl14	G	A	3: 123,165,043 (GRCm39)	T316I	probably damaging	Het
Mmp15	A	T	8: 96,098,945 (GRCm39)	N591Y	probably benign	Het
Mrpl53	T	C	6: 83,086,518 (GRCm39)	L74P	probably damaging	Het
Mvp	C	T	7: 126,589,037 (GRCm39)	V577M	probably damaging	Het
Neb	T	C	2: 52,139,388 (GRCm39)	K140E	probably damaging	Het
Ngf	G	T	3: 102,417,119 (GRCm39)		probably benign	Het
Nipsnap3b	C	T	4: 53,017,088 (GRCm39)	A104V	possibly damaging	Het
Nlrp14	A	G	7: 106,781,928 (GRCm39)	Y375C	probably benign	Het
Nod1	A	G	6: 54,915,202 (GRCm39)	Y764H	probably damaging	Het
Or13d1	A	T	4: 52,971,232 (GRCm39)	I204F	probably benign	Het
Or2w25	G	A	11: 59,504,320 (GRCm39)	V177M	probably damaging	Het
Or7e177	T	G	9: 20,212,387 (GRCm39)	M297R	probably damaging	Het
Pcdhb19	A	T	18: 37,630,235 (GRCm39)	Q10L	probably benign	Het
Pdcl	T	C	2: 37,242,142 (GRCm39)	I203V	probably benign	Het
Peg10	C	A	6: 4,755,711 (GRCm39)	R96S	possibly damaging	Het
Pknox1	T	A	17: 31,823,764 (GRCm39)	N379K	probably benign	Het
Prodh	T	G	16: 17,895,677 (GRCm39)	Q360P	probably damaging	Het
Raf1	C	T	6: 115,609,934 (GRCm39)	G202S	probably benign	Het
Rgs11	T	A	17: 26,426,433 (GRCm39)		probably null	Het
Rilp	A	T	11: 75,401,059 (GRCm39)	H29L	probably damaging	Het
Rtel1	T	C	2: 180,962,839 (GRCm39)	C31R	probably damaging	Het
Rubcnl	T	A	14: 75,279,898 (GRCm39)	I427K	probably damaging	Het
Ryr1	C	A	7: 28,751,460 (GRCm39)	R3706L	probably damaging	Het
Ryr2	T	C	13: 11,729,434 (GRCm39)	D2396G	probably damaging	Het
Slc45a2	T	C	15: 11,025,954 (GRCm39)	S435P	probably damaging	Het
Spata17	A	G	1: 186,844,798 (GRCm39)	V111A	probably damaging	Het
Svep1	C	T	4: 58,116,608 (GRCm39)	D881N	possibly damaging	Het
Sypl2	T	A	3: 108,126,411 (GRCm39)	N67I	possibly damaging	Het
Tenm3	T	C	8: 48,689,755 (GRCm39)	Y1944C	probably damaging	Het
Tep1	A	T	14: 51,062,246 (GRCm39)	D2535E	possibly damaging	Het
Tkt	T	A	14: 30,294,177 (GRCm39)	I529N	probably damaging	Het
Trp53i11	T	G	2: 93,028,080 (GRCm39)	V39G	probably damaging	Het
Trpm2	C	T	10: 77,761,659 (GRCm39)	G997D	probably damaging	Het
Usp3	A	G	9: 66,447,449 (GRCm39)	V219A	possibly damaging	Het
Usp4	T	A	9: 108,268,870 (GRCm39)		probably null	Het
Wdfy3	A	G	5: 102,065,277 (GRCm39)	V1297A	probably benign	Het
Wdr46	T	A	17: 34,159,997 (GRCm39)	F70I	probably benign	Het
Xkr6	T	C	14: 64,056,998 (GRCm39)	V303A	unknown	Het
Zdbf2	C	T	1: 63,343,165 (GRCm39)	Q515*	probably null	Het
Zfhx2	A	G	14: 55,310,354 (GRCm39)	Y731H	possibly damaging	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
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
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'- TTGGCATGGGACACTGGCATAC -3'
(R):5'- AGGAACTGCTGATGCAGCATGAC -3'

Sequencing Primer
(F):5'- GCATACTGGCCTCAGAGACAG -3'
(R):5'- GGAGTCCACACCTTTGAAAGTTC -3'

Posted On

2013-07-24