Mutagenetix > Incidental Mutation

Incidental Mutation 'R8377:Nfya'

646779

Institutional Source

Beutler Lab

Gene Symbol

Nfya

Ensembl Gene

ENSMUSG00000023994

Gene Name

nuclear transcription factor-Y alpha

Synonyms

Sez10, Cbf-b

MMRRC Submission

067745-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8377 (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 G at 48699073 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 240 (V240A)

Ref Sequence

ENSEMBL: ENSMUSP00000043909 (fasta)

Gene Model

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

AlphaFold

P23708

Predicted Effect

possibly damaging
Transcript: ENSMUST00000046719
AA Change: V240A

PolyPhen 2 Score 0.923 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000043909
Gene: ENSMUSG00000023994
AA Change: V240A

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

possibly damaging
Transcript: ENSMUST00000078800
AA Change: V239A

PolyPhen 2 Score 0.923 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000077853
Gene: ENSMUSG00000023994
AA Change: V239A

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: V205A

SMART Domains

Protein: ENSMUSP00000124404
Gene: ENSMUSG00000023994
AA Change: V205A

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: V100A

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: V232A

SMART Domains

Protein: ENSMUSP00000124501
Gene: ENSMUSG00000023994
AA Change: V232A

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

possibly damaging
Transcript: ENSMUST00000160319
AA Change: V234A

PolyPhen 2 Score 0.909 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000124245
Gene: ENSMUSG00000023994
AA Change: V234A

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

possibly damaging
Transcript: ENSMUST00000161117
AA Change: V205A

PolyPhen 2 Score 0.923 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000124965
Gene: ENSMUSG00000023994
AA Change: V205A

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: ENSMUST00000161256
AA Change: V104A

PolyPhen 2 Score 0.505 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000125034
Gene: ENSMUSG00000023994
AA Change: V104A

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: V211A

SMART Domains

Protein: ENSMUSP00000123785
Gene: ENSMUSG00000023994
AA Change: V211A

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: 99.7%
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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acot3	C	A	12: 84,105,561 (GRCm39)	C251*	probably null	Het
Acsbg1	A	G	9: 54,529,789 (GRCm39)	C273R	probably damaging	Het
Adh6a	A	G	3: 138,031,884 (GRCm39)	T259A	probably damaging	Het
Aknad1	A	G	3: 108,689,255 (GRCm39)	H639R	possibly damaging	Het
Alkal2	G	T	12: 30,934,850 (GRCm39)	G23V	probably damaging	Het
Ampd3	A	G	7: 110,399,937 (GRCm39)	R342G	probably damaging	Het
Arid5b	G	T	10: 67,933,217 (GRCm39)	A895E	probably damaging	Het
BB014433	GCACACAGCTTTGGAGGTGTACACACCCGGGTTGGGGCCTCTACACACAGCTTTGGAGGTGTACACACCCGGGTTGGGGCCTCTGCACACAGCTTTGG	GCACACAGCTTTGGAGGTGTACACACCCGGGTTGGGGCCTCTGCACACAGCTTTGG	8: 15,092,160 (GRCm39)		probably benign	Het
Bmp8a	G	T	4: 123,236,482 (GRCm39)	P7Q	unknown	Het
Boll	A	C	1: 55,362,837 (GRCm39)	V187G	possibly damaging	Het
Ccdc162	A	T	10: 41,457,306 (GRCm39)	C1544S	probably benign	Het
Cmss1	A	C	16: 57,127,757 (GRCm39)	M182R	possibly damaging	Het
Cntn3	T	C	6: 102,186,254 (GRCm39)	M578V	probably benign	Het
Dmxl2	A	T	9: 54,286,032 (GRCm39)	W2718R	probably damaging	Het
Dsg1a	T	A	18: 20,466,831 (GRCm39)	I567N	probably damaging	Het
Epc2	T	A	2: 49,412,527 (GRCm39)	D168E	probably damaging	Het
Ern2	G	A	7: 121,780,515 (GRCm39)	Q162*	probably null	Het
F11r	G	T	1: 171,265,111 (GRCm39)		probably benign	Het
Fcgrt	T	C	7: 44,751,987 (GRCm39)	Y59C	probably damaging	Het
Fmn2	G	T	1: 174,436,011 (GRCm39)	E661*	probably null	Het
Gbp4	T	A	5: 105,266,328 (GRCm39)	Q571L	probably benign	Het
Gm29106	A	T	1: 118,126,593 (GRCm39)	H95L	probably damaging	Het
Gphn	G	A	12: 78,711,280 (GRCm39)	V621M	probably damaging	Het
Grwd1	T	C	7: 45,480,036 (GRCm39)	Y57C	probably damaging	Het
Insyn2b	C	A	11: 34,351,964 (GRCm39)	A2D	probably damaging	Het
Irs2	G	A	8: 11,054,848 (GRCm39)	Q1195*	probably null	Het
Itpr1	G	C	6: 108,487,699 (GRCm39)	C2375S	probably benign	Het
Kcnmb4	A	T	10: 116,282,290 (GRCm39)	Y136N	probably benign	Het
Matn2	C	T	15: 34,345,511 (GRCm39)	P173S	probably damaging	Het
Med17	A	C	9: 15,173,655 (GRCm39)	D606E	probably damaging	Het
Mpl	A	G	4: 118,301,254 (GRCm39)	V537A		Het
Mrpl1	C	G	5: 96,374,226 (GRCm39)	A167G	probably benign	Het
Mrpl21	T	C	19: 3,342,487 (GRCm39)	F206S	unknown	Het
Msh6	T	A	17: 88,292,598 (GRCm39)	M451K	probably damaging	Het
Myo10	T	C	15: 25,804,481 (GRCm39)	I1592T	possibly damaging	Het
Naip1	A	T	13: 100,562,374 (GRCm39)	D930E	possibly damaging	Het
Necap2	T	C	4: 140,795,534 (GRCm39)	I242V	probably benign	Het
Olfml2b	A	G	1: 170,496,353 (GRCm39)	D328G	probably damaging	Het
Or10ak13	A	T	4: 118,639,203 (GRCm39)	M193K	probably benign	Het
Or4k35	T	A	2: 111,099,983 (GRCm39)	H243L	probably damaging	Het
Or5b24	T	G	19: 12,912,399 (GRCm39)	V99G	probably benign	Het
Or5p53	T	G	7: 107,532,892 (GRCm39)	L55R	probably damaging	Het
Phf8-ps	C	A	17: 33,286,038 (GRCm39)	A255S	probably benign	Het
Pkd1l3	T	C	8: 110,361,982 (GRCm39)	V1018A	probably benign	Het
Plcg1	T	C	2: 160,596,842 (GRCm39)	L761P	probably damaging	Het
Ppp1r36	T	C	12: 76,485,215 (GRCm39)	S313P	possibly damaging	Het
Ptpru	C	A	4: 131,535,646 (GRCm39)	G444C	probably damaging	Het
Rfxank	A	T	8: 70,587,960 (GRCm39)	V149D	probably damaging	Het
Rimbp2	G	A	5: 128,857,395 (GRCm39)	H819Y	probably damaging	Het
Sgms1	T	C	19: 32,101,821 (GRCm39)	Y395C	probably damaging	Het
Siae	G	A	9: 37,542,901 (GRCm39)		probably null	Het
Slc46a2	T	A	4: 59,914,713 (GRCm39)	D70V	probably damaging	Het
Smpdl3a	A	C	10: 57,677,032 (GRCm39)	L43F	possibly damaging	Het
Spcs1	T	A	14: 30,722,103 (GRCm39)	D146V	possibly damaging	Het
Srcin1	T	C	11: 97,442,804 (GRCm39)	D8G	probably damaging	Het
Stra6	G	T	9: 58,056,488 (GRCm39)	L373F	probably damaging	Het
Tacc1	A	T	8: 25,672,299 (GRCm39)	S310T	possibly damaging	Het
Tlr12	T	C	4: 128,509,566 (GRCm39)	S895G	probably benign	Het
Tnfaip3	A	G	10: 18,887,258 (GRCm39)	V89A	probably damaging	Het
Top1	C	T	2: 160,488,009 (GRCm39)		probably benign	Het
Trappc13	T	G	13: 104,297,509 (GRCm39)	I132L	probably benign	Het
Trpt1	C	T	19: 6,976,349 (GRCm39)	Q249*	probably null	Het
Tsnaxip1	A	C	8: 106,569,179 (GRCm39)	K510Q	probably damaging	Het
Usp39	A	T	6: 72,305,657 (GRCm39)	N375K	probably benign	Het
Vldlr	T	A	19: 27,212,258 (GRCm39)	C91S	probably damaging	Het
Vmn1r232	T	A	17: 21,134,239 (GRCm39)	L120F	probably benign	Het
Vmn2r71	T	C	7: 85,264,707 (GRCm39)	V13A	probably benign	Het
Wdr11	T	A	7: 129,208,412 (GRCm39)	V389E	possibly damaging	Het
Wsb2	A	T	5: 117,514,766 (GRCm39)	I321F	possibly damaging	Het
Zan	A	T	5: 137,389,949 (GRCm39)	V4841E	unknown	Het
Zfy1	A	T	Y: 725,723 (GRCm39)	F681I	possibly damaging	Het
Zpld1	C	A	16: 55,067,017 (GRCm39)	E179D	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
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
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'- AGAACTGCACTGCTTCCTGC -3'
(R):5'- CGCTAACGTCATCCTTAAGGC -3'

Sequencing Primer
(F):5'- TGCTTAGCACTCCCCAGG -3'
(R):5'- GTCATCCTTAAGGCACTAGCAG -3'

Posted On

2020-09-02