Mutagenetix > Incidental Mutation

Incidental Mutation 'R7554:Ift56'

584609

Institutional Source

Beutler Lab

Gene Symbol

Ift56

Ensembl Gene

ENSMUSG00000056832

Gene Name

intraflagellar transport 56

Synonyms

hpy, hydrocephalic-polydactyl, 9430097H08Rik, hop, Ttc26

MMRRC Submission

045651-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.583) question?

Stock #

R7554 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

38358404-38404582 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 38362435 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 70 (L70Q)

Ref Sequence

ENSEMBL: ENSMUSP00000124369 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000159145] [ENSMUST00000160215] [ENSMUST00000161751] [ENSMUST00000162554]

AlphaFold

Q8BS45

Predicted Effect

probably damaging
Transcript: ENSMUST00000159145
AA Change: L70Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000124873
Gene: ENSMUSG00000056832
AA Change: L70Q

Domain	Start	End	E-Value	Type
low complexity region	19	29	N/A	INTRINSIC
Pfam:TPR_2	58	88	1.2e-5	PFAM
Pfam:TPR_8	58	91	1.7e-3	PFAM
Pfam:TPR_1	61	87	4.6e-4	PFAM
Pfam:TPR_11	63	113	4.9e-11	PFAM
Pfam:TPR_19	67	113	3.1e-7	PFAM
Pfam:TPR_8	89	113	2e-3	PFAM
Pfam:TPR_1	91	113	1.7e-4	PFAM
Pfam:TPR_2	91	113	2.4e-3	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000160215
AA Change: L70Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000125097
Gene: ENSMUSG00000056832
AA Change: L70Q

Domain	Start	End	E-Value	Type
low complexity region	19	29	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000161751
AA Change: L70Q

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000124271
Gene: ENSMUSG00000056832
AA Change: L70Q

Domain	Start	End	E-Value	Type
low complexity region	19	29	N/A	INTRINSIC
Pfam:TPR_2	58	88	1.3e-5	PFAM
Pfam:TPR_8	58	91	1.8e-3	PFAM
Pfam:TPR_6	59	87	2.6e-3	PFAM
Pfam:TPR_1	61	87	4.8e-4	PFAM
Pfam:TPR_11	63	115	4.1e-11	PFAM
Pfam:TPR_19	67	130	1.7e-7	PFAM
Pfam:TPR_8	89	113	2.1e-3	PFAM
Pfam:TPR_1	91	113	1.8e-4	PFAM
Pfam:TPR_2	91	113	2.5e-3	PFAM
Pfam:TPR_9	145	210	9.4e-4	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000162554
AA Change: L70Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000124369
Gene: ENSMUSG00000056832
AA Change: L70Q

Domain	Start	End	E-Value	Type
low complexity region	19	29	N/A	INTRINSIC
Pfam:TPR_2	58	88	2.7e-5	PFAM
Pfam:TPR_11	63	117	9e-9	PFAM
Pfam:TPR_9	157	227	9.2e-4	PFAM
Blast:TPR	359	392	9e-10	BLAST
Blast:TPR	461	494	8e-15	BLAST

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Mice homozygous for a spontaneous nonsense mutation exhibit partial prenatal lethality, a hopping gait, preaxial polydactyly, male sterility due to lack of sperm flagella, impaired hearing, and patterning defects that are typical of impaired Hedgehog signaling. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5031439G07Rik	A	T	15: 84,839,686 (GRCm39)	F185I	probably damaging	Het
Abi3bp	T	A	16: 56,438,575 (GRCm39)		probably null	Het
Acot5	T	A	12: 84,120,254 (GRCm39)	L203H	probably damaging	Het
Alad	C	T	4: 62,430,023 (GRCm39)		probably null	Het
Alkbh5	C	T	11: 60,429,415 (GRCm39)	T56I	probably benign	Het
Apbb1ip	G	A	2: 22,713,558 (GRCm39)	D138N	unknown	Het
BC049715	T	G	6: 136,817,295 (GRCm39)	S178R	probably damaging	Het
C1rb	C	A	6: 124,557,365 (GRCm39)	H501N	probably damaging	Het
Celsr3	A	T	9: 108,718,408 (GRCm39)	M2327L	probably benign	Het
Cers4	G	A	8: 4,565,718 (GRCm39)	V55I	probably benign	Het
Cngb3	A	T	4: 19,461,753 (GRCm39)	K545*	probably null	Het
Crb1	C	T	1: 139,265,019 (GRCm39)	C133Y	probably damaging	Het
Cryba4	C	T	5: 112,398,969 (GRCm39)	R25Q	probably damaging	Het
Cyp7b1	C	T	3: 18,151,610 (GRCm39)	G201D	probably benign	Het
Dcun1d2	A	T	8: 13,331,077 (GRCm39)	C18S	probably benign	Het
Ddx39b	A	T	17: 35,466,006 (GRCm39)	I176F	probably benign	Het
Dnah7a	A	G	1: 53,567,857 (GRCm39)	I1913T	possibly damaging	Het
Eif2ak1	T	C	5: 143,816,296 (GRCm39)	I198T	probably damaging	Het
Esp34	G	A	17: 38,866,782 (GRCm39)	M75I	probably benign	Het
Fam98a	G	T	17: 75,854,670 (GRCm39)	C46*	probably null	Het
Fanci	A	T	7: 79,062,500 (GRCm39)	N342I	probably damaging	Het
Fat1	A	T	8: 45,490,202 (GRCm39)	I3705F	possibly damaging	Het
Fbxw7	T	A	3: 84,883,620 (GRCm39)	V598D		Het
Gas2l2	G	A	11: 83,315,236 (GRCm39)	Q306*	probably null	Het
Gbp10	G	A	5: 105,384,015 (GRCm39)		probably benign	Het
Gigyf2	T	A	1: 87,335,292 (GRCm39)	S378T	unknown	Het
Hao1	C	T	2: 134,372,538 (GRCm39)	V157M	possibly damaging	Het
Hdlbp	C	T	1: 93,365,031 (GRCm39)	V79M	probably damaging	Het
Htt	G	A	5: 35,022,084 (GRCm39)	R1676H	probably damaging	Het
Klhl11	A	G	11: 100,354,774 (GRCm39)	V349A	probably benign	Het
Lama2	T	C	10: 27,031,492 (GRCm39)	E1522G	probably damaging	Het
Map3k4	T	A	17: 12,451,300 (GRCm39)	K1531M	probably damaging	Het
Map3k4	T	A	17: 12,451,301 (GRCm39)	K1531*	probably null	Het
Mapk15	A	G	15: 75,867,745 (GRCm39)	Y120C	possibly damaging	Het
Mapt	C	A	11: 104,189,528 (GRCm39)	P182Q	probably benign	Het
Mgat4d	A	C	8: 84,082,402 (GRCm39)	K117N	probably benign	Het
Mid1	G	T	X: 168,769,010 (GRCm39)	S468I	possibly damaging	Het
Mmp8	T	C	9: 7,563,112 (GRCm39)	L225P	probably damaging	Het
Mrps31	A	G	8: 22,911,445 (GRCm39)	K229R	possibly damaging	Het
Muc5b	A	T	7: 141,412,513 (GRCm39)	T1820S	unknown	Het
Myof	T	C	19: 37,942,958 (GRCm39)	T707A	probably benign	Het
Nckap5l	A	T	15: 99,327,261 (GRCm39)	S143T	probably benign	Het
Notch3	A	G	17: 32,341,345 (GRCm39)	S2136P	probably benign	Het
Nphp3	A	T	9: 103,919,270 (GRCm39)	D1306V	probably damaging	Het
Or10ag56	T	A	2: 87,139,349 (GRCm39)	M92K	probably damaging	Het
Or1e1b-ps1	C	T	11: 73,845,630 (GRCm39)	T38I	probably damaging	Het
Or2at1	T	A	7: 99,417,210 (GRCm39)	N280K	possibly damaging	Het
Or52n1	T	C	7: 104,383,074 (GRCm39)	I166V	probably benign	Het
Or56b1	T	C	7: 104,285,733 (GRCm39)	M284T	probably benign	Het
Or5k15	T	C	16: 58,709,769 (GRCm39)	I271M	probably benign	Het
Pabpc4l	T	A	3: 46,401,549 (GRCm39)	T32S	probably benign	Het
Pcdhb10	A	C	18: 37,544,935 (GRCm39)	T4P	probably benign	Het
Pkhd1l1	A	G	15: 44,358,866 (GRCm39)	I358M	probably damaging	Het
Plekhg1	A	G	10: 3,913,647 (GRCm39)	E1178G		Het
Prkcd	A	T	14: 30,331,220 (GRCm39)	Y52N	probably damaging	Het
Rasa3	G	A	8: 13,645,390 (GRCm39)	T183M	probably damaging	Het
Rbm26	G	T	14: 105,398,029 (GRCm39)	A31D	unknown	Het
Scara3	T	C	14: 66,158,299 (GRCm39)	T570A	possibly damaging	Het
Sec24d	T	A	3: 123,149,423 (GRCm39)	V810D	probably damaging	Het
Sgcz	A	T	8: 38,030,426 (GRCm39)		probably null	Het
Stt3b	A	G	9: 115,109,477 (GRCm39)		probably null	Het
Synpo	G	T	18: 60,736,405 (GRCm39)	Q514K	probably benign	Het
Tagln2	G	T	1: 172,333,411 (GRCm39)	K88N	probably damaging	Het
Tcaf1	T	A	6: 42,654,388 (GRCm39)	K601N	probably benign	Het
Tent4a	G	T	13: 69,648,191 (GRCm39)	H734Q	probably damaging	Het
Tprn	T	C	2: 25,153,811 (GRCm39)	F371S	probably damaging	Het
Ttn	A	T	2: 76,671,652 (GRCm39)	V11304E	unknown	Het
Ttn	C	T	2: 76,706,207 (GRCm39)	W9171*	probably null	Het
Vmn2r50	A	T	7: 9,784,066 (GRCm39)	M136K	probably null	Het
Zfp518b	G	A	5: 38,830,415 (GRCm39)	P530L	probably damaging	Het
Zfp941	C	A	7: 140,391,970 (GRCm39)	S463I	possibly damaging	Het

Other mutations in Ift56

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00927:Ift56	APN	6	38,359,155 (GRCm39)	splice site	probably benign
IGL02049:Ift56	APN	6	38,402,067 (GRCm39)	missense	probably benign	0.16
IGL02403:Ift56	APN	6	38,386,373 (GRCm39)	missense	possibly damaging	0.95
IGL02902:Ift56	APN	6	38,402,097 (GRCm39)	missense	probably benign	0.21
IGL03189:Ift56	APN	6	38,402,166 (GRCm39)	missense	probably benign	0.00
IGL03410:Ift56	APN	6	38,362,435 (GRCm39)	missense	probably damaging	1.00
R0346:Ift56	UTSW	6	38,386,370 (GRCm39)	missense	probably damaging	1.00
R0562:Ift56	UTSW	6	38,378,064 (GRCm39)	missense	probably damaging	1.00
R0826:Ift56	UTSW	6	38,402,049 (GRCm39)	splice site	probably null
R1212:Ift56	UTSW	6	38,387,728 (GRCm39)	missense	probably damaging	1.00
R1778:Ift56	UTSW	6	38,386,411 (GRCm39)	missense	possibly damaging	0.93
R1972:Ift56	UTSW	6	38,387,738 (GRCm39)	missense	probably benign	0.20
R2903:Ift56	UTSW	6	38,378,037 (GRCm39)	missense	possibly damaging	0.61
R2904:Ift56	UTSW	6	38,378,037 (GRCm39)	missense	possibly damaging	0.61
R2905:Ift56	UTSW	6	38,378,037 (GRCm39)	missense	possibly damaging	0.61
R3788:Ift56	UTSW	6	38,380,459 (GRCm39)	critical splice donor site	probably null
R4222:Ift56	UTSW	6	38,372,010 (GRCm39)	missense	probably damaging	1.00
R4392:Ift56	UTSW	6	38,358,492 (GRCm39)	start gained	probably benign
R4930:Ift56	UTSW	6	38,368,475 (GRCm39)	missense	probably damaging	1.00
R5484:Ift56	UTSW	6	38,366,057 (GRCm39)	missense	probably benign	0.10
R5920:Ift56	UTSW	6	38,389,005 (GRCm39)	missense	probably damaging	1.00
R6229:Ift56	UTSW	6	38,371,975 (GRCm39)	missense	probably benign	0.22
R6429:Ift56	UTSW	6	38,375,248 (GRCm39)	missense	possibly damaging	0.69
R6901:Ift56	UTSW	6	38,378,079 (GRCm39)	missense	possibly damaging	0.80
R7448:Ift56	UTSW	6	38,381,422 (GRCm39)	nonsense	probably null
R7650:Ift56	UTSW	6	38,371,975 (GRCm39)	missense	probably benign	0.22
R8319:Ift56	UTSW	6	38,382,880 (GRCm39)	missense	probably damaging	0.98
R9270:Ift56	UTSW	6	38,366,109 (GRCm39)	intron	probably benign
R9417:Ift56	UTSW	6	38,386,386 (GRCm39)	missense	probably damaging	1.00
X0066:Ift56	UTSW	6	38,382,877 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- TGAGCTGCGAGTATTGTCCAG -3'
(R):5'- GCCTGTATTAAAAGACATAGGGC -3'

Sequencing Primer
(F):5'- GCGAGTATTGTCCAGCCTCTATTAG -3'
(R):5'- CTGTATTAAAAGACATAGGGCTGGGG -3'

Posted On

2019-10-17