Mutagenetix > Incidental Mutation

Incidental Mutation 'R9321:Nfya'

706237

Institutional Source

Beutler Lab

Gene Symbol

Nfya

Ensembl Gene

ENSMUSG00000023994

Gene Name

nuclear transcription factor-Y alpha

Synonyms

Sez10, Cbf-b

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9321 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

48693917-48716782 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 48707494 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glutamic Acid at position 16 (V16E)

Ref Sequence

ENSEMBL: ENSMUSP00000043909 (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: V16E

SMART Domains

Protein: ENSMUSP00000043909
Gene: ENSMUSG00000023994
AA Change: V16E

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: V16E

SMART Domains

Protein: ENSMUSP00000077853
Gene: ENSMUSG00000023994
AA Change: V16E

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

possibly damaging
Transcript: ENSMUST00000159063
AA Change: V16E

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000124404
Gene: ENSMUSG00000023994
AA Change: V16E

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: V16E

PolyPhen 2 Score 0.915 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000124501
Gene: ENSMUSG00000023994
AA Change: V16E

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: V16E

SMART Domains

Protein: ENSMUSP00000124245
Gene: ENSMUSG00000023994
AA Change: V16E

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

possibly damaging
Transcript: ENSMUST00000162460
AA Change: V16E

PolyPhen 2 Score 0.915 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000123785
Gene: ENSMUSG00000023994
AA Change: V16E

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: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

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: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	A	G	11: 9,460,475 (GRCm39)	S4162G	probably benign	Het
Acvr2b	T	C	9: 119,257,351 (GRCm39)	I152T	probably benign	Het
Adam15	T	A	3: 89,254,794 (GRCm39)		probably null	Het
Adam34	C	T	8: 44,105,243 (GRCm39)	G134D	probably damaging	Het
Aifm2	C	T	10: 61,571,410 (GRCm39)	Q315*	probably null	Het
Akap10	A	G	11: 61,791,235 (GRCm39)	F408S	probably damaging	Het
Ap3b2	T	C	7: 81,114,252 (GRCm39)		probably null	Het
Btbd2	A	C	10: 80,483,675 (GRCm39)	V181G	probably damaging	Het
Carmil3	G	T	14: 55,741,425 (GRCm39)	G1070V		Het
Ceacam2	G	T	7: 25,230,089 (GRCm39)	D172E	possibly damaging	Het
Crtc3	G	A	7: 80,259,650 (GRCm39)	A203V	probably benign	Het
Dclre1a	A	G	19: 56,531,100 (GRCm39)	S749P	probably damaging	Het
Dnah2	C	T	11: 69,338,939 (GRCm39)		probably null	Het
Eif2ak4	G	A	2: 118,292,798 (GRCm39)	V1341M	possibly damaging	Het
Enpp5	T	C	17: 44,393,689 (GRCm39)	V295A	possibly damaging	Het
Gm1110	T	A	9: 26,831,891 (GRCm39)	M87L	probably benign	Het
Gm57858	A	T	3: 36,073,139 (GRCm39)	V381E	probably damaging	Het
H2-Ab1	T	C	17: 34,486,969 (GRCm39)	L241P	probably damaging	Het
Hmx2	A	G	7: 131,157,320 (GRCm39)	T145A	probably benign	Het
Irag1	A	G	7: 110,524,534 (GRCm39)	S138P	probably benign	Het
Itpripl1	T	C	2: 126,984,000 (GRCm39)	S41G	probably benign	Het
Kcnb2	G	A	1: 15,779,793 (GRCm39)	D222N	possibly damaging	Het
Ldb3	C	A	14: 34,266,099 (GRCm39)	G499*	probably null	Het
Lig1	T	C	7: 13,034,935 (GRCm39)	F577S	probably damaging	Het
Lnx1	T	C	5: 74,780,991 (GRCm39)	I177V	probably damaging	Het
Mark4	G	T	7: 19,170,901 (GRCm39)	T323K	probably benign	Het
Mroh5	A	G	15: 73,661,113 (GRCm39)	V301A	probably benign	Het
Mtx3	T	A	13: 92,984,097 (GRCm39)	W125R	probably damaging	Het
Myo18a	G	A	11: 77,733,370 (GRCm39)	G1404R	probably damaging	Het
Myom2	C	T	8: 15,172,464 (GRCm39)	P1188S	possibly damaging	Het
Nars1	C	T	18: 64,637,950 (GRCm39)	E335K	probably damaging	Het
Nicn1	C	T	9: 108,171,708 (GRCm39)	R163C	possibly damaging	Het
Nlrp4e	C	G	7: 23,020,755 (GRCm39)	A414G	probably benign	Het
Nme5	T	G	18: 34,704,597 (GRCm39)	I83L	probably benign	Het
Nos1	G	C	5: 118,017,402 (GRCm39)	R255P	probably benign	Het
Nptx1	A	G	11: 119,438,378 (GRCm39)	L13P	unknown	Het
Or11g27	G	A	14: 50,771,471 (GRCm39)	V201I	probably benign	Het
Or13c25	G	T	4: 52,911,314 (GRCm39)	T160N	probably damaging	Het
Or13m2-ps1	T	A	6: 42,777,792 (GRCm39)	V39D	possibly damaging	Het
Or4k44	A	G	2: 111,368,434 (GRCm39)	S67P	probably damaging	Het
Or5j3	A	T	2: 86,128,297 (GRCm39)	I46F	probably benign	Het
Or6d13	T	C	6: 116,518,370 (GRCm39)	Y319H	probably benign	Het
Pdzd2	T	C	15: 12,386,023 (GRCm39)	T916A	probably benign	Het
Plekha6	A	G	1: 133,209,549 (GRCm39)	N615S	probably damaging	Het
Prorp	A	G	12: 55,351,434 (GRCm39)	I248V	possibly damaging	Het
Rad52	T	C	6: 119,889,969 (GRCm39)	Y32H	probably damaging	Het
Slc22a16	T	A	10: 40,450,047 (GRCm39)	I161N	probably damaging	Het
Slx4	A	G	16: 3,804,654 (GRCm39)	M720T	probably benign	Het
Spem1	T	C	11: 69,712,661 (GRCm39)	H58R	probably benign	Het
Spg7	C	A	8: 123,803,688 (GRCm39)	D239E	probably benign	Het
Tas2r123	A	T	6: 132,825,095 (GRCm39)	M331L	probably benign	Het
Tcaf1	T	C	6: 42,656,290 (GRCm39)	T229A	probably benign	Het
Tdrd1	T	C	19: 56,848,767 (GRCm39)	L939P	probably damaging	Het
Timd2	T	C	11: 46,577,916 (GRCm39)	T72A	probably benign	Het
Tmem179	G	T	12: 112,477,390 (GRCm39)	N31K	probably damaging	Het
Tpd52l1	T	C	10: 31,214,189 (GRCm39)	S165G		Het
Tubgcp6	T	C	15: 88,992,186 (GRCm39)	T600A	probably damaging	Het
Txlna	T	A	4: 129,528,246 (GRCm39)	E230D	probably damaging	Het
Ush2a	A	T	1: 188,089,148 (GRCm39)	I368F	probably damaging	Het
Vmn1r76	A	T	7: 11,665,094 (GRCm39)	M40K	possibly damaging	Het
Zfp592	C	T	7: 80,691,226 (GRCm39)	S1135L	possibly damaging	Het
Zfp606	A	G	7: 12,226,610 (GRCm39)	T244A	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
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
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
Z1177:Nfya	UTSW	17	48,700,541 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- ACAAGTACCAGGTGGCAAC -3'
(R):5'- TGAGCATCTCCCAATGGTGC -3'

Sequencing Primer
(F):5'- GGCAACAGACTGATTCATTGC -3'
(R):5'- AGTAGGTATCTTAAGAGGGCCTTTAC -3'

Posted On

2022-04-18