Mutagenetix > Incidental Mutation

Incidental Mutation 'R6009:Crlf1'

479654

Institutional Source

Beutler Lab

Gene Symbol

Crlf1

Ensembl Gene

ENSMUSG00000007888

Gene Name

cytokine receptor-like factor 1

Synonyms

cytokine receptor like molecule 3, CRLM3, CLF-1

MMRRC Submission

044186-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.820) question?

Stock #

R6009 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

70945808-70956731 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 70956129 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Threonine at position 403 (K403T)

Ref Sequence

ENSEMBL: ENSMUSP00000008032 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000008032] [ENSMUST00000075175] [ENSMUST00000081940] [ENSMUST00000121623] [ENSMUST00000124967] [ENSMUST00000125184] [ENSMUST00000138260] [ENSMUST00000129909] [ENSMUST00000136913] [ENSMUST00000140679] [ENSMUST00000165126] [ENSMUST00000135446] [ENSMUST00000132648]

AlphaFold

Q9JM58

Predicted Effect

probably damaging
Transcript: ENSMUST00000008032
AA Change: K403T

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000008032
Gene: ENSMUSG00000007888
AA Change: K403T

Domain	Start	End	E-Value	Type
signal peptide	1	40	N/A	INTRINSIC
Pfam:Lep_receptor_Ig	41	127	5.7e-8	PFAM
FN3	138	223	2.11e0	SMART
FN3	238	323	1.5e-5	SMART
low complexity region	345	361	N/A	INTRINSIC
low complexity region	415	425	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000075175

SMART Domains

Protein: ENSMUSP00000074670
Gene: ENSMUSG00000058833

Domain	Start	End	E-Value	Type
Pfam:DNA_repr_REX1B	29	128	1.5e-27	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000081940

SMART Domains

Protein: ENSMUSP00000080608
Gene: ENSMUSG00000090137

Domain	Start	End	E-Value	Type
UBQ	1	72	2.14e-36	SMART
Pfam:Ribosomal_L40e	77	128	4.5e-33	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000121623

SMART Domains

Protein: ENSMUSP00000113804
Gene: ENSMUSG00000055553

Domain	Start	End	E-Value	Type
Pfam:KxDL	14	99	3.3e-34	PFAM
UBQ	105	176	2.14e-36	SMART
Ribosomal_L40e	181	232	1.02e-31	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000124967

SMART Domains

Protein: ENSMUSP00000122797
Gene: ENSMUSG00000090137

Domain	Start	End	E-Value	Type
UBQ	1	72	2.14e-36	SMART
Pfam:Ribosomal_L40e	77	96	5e-9	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000125184

SMART Domains

Protein: ENSMUSP00000120096
Gene: ENSMUSG00000090137

Domain	Start	End	E-Value	Type
UBQ	1	72	2.14e-36	SMART
Pfam:Ribosomal_L40e	77	128	4.5e-33	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127793

Predicted Effect

unknown
Transcript: ENSMUST00000127983
AA Change: K107T

SMART Domains

Protein: ENSMUSP00000115614
Gene: ENSMUSG00000007888
AA Change: K107T

Domain	Start	End	E-Value	Type
Blast:FN3	2	28	2e-12	BLAST
SCOP:d1eerb2	2	46	1e-8	SMART
low complexity region	50	66	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000143598

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128620

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132107

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135773

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133683

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138196

Predicted Effect

probably benign
Transcript: ENSMUST00000138260

SMART Domains

Protein: ENSMUSP00000123438
Gene: ENSMUSG00000055553

Domain	Start	End	E-Value	Type
Pfam:KxDL	12	99	9.2e-40	PFAM
UBQ	105	176	2.14e-36	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000129909

SMART Domains

Protein: ENSMUSP00000121149
Gene: ENSMUSG00000090137

Domain	Start	End	E-Value	Type
UBQ	1	72	2.14e-36	SMART
Ribosomal_L40e	77	128	1.02e-31	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000136913

SMART Domains

Protein: ENSMUSP00000120446
Gene: ENSMUSG00000058833

Domain	Start	End	E-Value	Type
Pfam:DNA_repr_REX1B	29	128	4.2e-28	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000140679

SMART Domains

Protein: ENSMUSP00000123263
Gene: ENSMUSG00000090137

Domain	Start	End	E-Value	Type
UBQ	1	72	2.14e-36	SMART
Pfam:Ribosomal_L40e	77	128	4.5e-33	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000165126

SMART Domains

Protein: ENSMUSP00000137461
Gene: ENSMUSG00000090137

Domain	Start	End	E-Value	Type
UBQ	1	72	2.14e-36	SMART
Pfam:Ribosomal_L40e	77	128	4.5e-33	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000135446

SMART Domains

Protein: ENSMUSP00000123562
Gene: ENSMUSG00000090137

Domain	Start	End	E-Value	Type
UBQ	1	72	2.14e-36	SMART
Pfam:Ribosomal_L40e	77	128	4.5e-33	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000132648

SMART Domains

Protein: ENSMUSP00000119545
Gene: ENSMUSG00000007888

Domain	Start	End	E-Value	Type
FN3	16	101	2.11e0	SMART
low complexity region	104	122	N/A	INTRINSIC

Meta Mutation Damage Score

0.3219

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.3%
20x: 91.5%

Validation Efficiency

100% (53/53)

MGI Phenotype

FUNCTION: This gene encodes a member of the cytokine type I receptor family. The encoded protein functions as a cytokine receptor subunit and may be involved in immune system regulation and fetal development. [provided by RefSeq, Dec 2015]
PHENOTYPE: Mice homozygous for a targeted mutation fail to suckle effectively and do not survive beyond 24 hrs after birth. Newborns exhibit reduced numbers of hematopoietic progenitor cells as well as a significant reduction in the number of motoneurons in the lumbar spinal cord and facial nucleus. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actr8	A	G	14: 29,700,454 (GRCm39)		probably benign	Het
Afap1	T	C	5: 36,154,904 (GRCm39)	S683P	probably damaging	Het
Chid1	T	A	7: 141,109,493 (GRCm39)	D131V	probably damaging	Het
Clstn2	C	T	9: 97,338,579 (GRCm39)	R860Q	probably benign	Het
Ctdspl2	T	G	2: 121,819,319 (GRCm39)	N201K	probably benign	Het
Cyb561a3	G	A	19: 10,564,172 (GRCm39)	V171I	possibly damaging	Het
Dazap1	T	C	10: 80,121,138 (GRCm39)		probably benign	Het
Dbf4	G	T	5: 8,453,718 (GRCm39)	Q235K	probably damaging	Het
Dgka	C	T	10: 128,559,548 (GRCm39)	G471D	probably damaging	Het
Fam13b	A	T	18: 34,630,458 (GRCm39)	F100Y	possibly damaging	Het
Flii	A	T	11: 60,611,583 (GRCm39)	L376*	probably null	Het
Fnip1	G	T	11: 54,393,097 (GRCm39)	G487V	probably damaging	Het
Gm7247	C	T	14: 51,601,805 (GRCm39)	S26F	probably benign	Het
Golgb1	G	T	16: 36,735,321 (GRCm39)	A1523S	probably damaging	Het
Gstm4	A	G	3: 107,950,659 (GRCm39)	V114A	possibly damaging	Het
Gtf3c1	A	G	7: 125,246,602 (GRCm39)	F1569S	possibly damaging	Het
Gtf3c5	A	T	2: 28,461,177 (GRCm39)	D312E	probably benign	Het
Gtpbp1	G	A	15: 79,596,297 (GRCm39)	V149M	probably damaging	Het
Hoxa7	C	T	6: 52,194,367 (GRCm39)	V7M	probably damaging	Het
Il17f	C	T	1: 20,849,510 (GRCm39)		probably null	Het
Ints9	T	C	14: 65,245,531 (GRCm39)	V263A	probably benign	Het
Kansl1l	C	T	1: 66,774,759 (GRCm39)	C689Y	probably benign	Het
Kctd7	G	A	5: 130,174,039 (GRCm39)	G39E	probably damaging	Het
Krt82	T	A	15: 101,453,540 (GRCm39)	D282V	probably benign	Het
Lemd1	G	T	1: 132,155,990 (GRCm39)	E11*	probably null	Het
Maml2	A	G	9: 13,532,294 (GRCm39)	T503A	probably benign	Het
Mief2	A	G	11: 60,622,485 (GRCm39)	T352A	probably benign	Het
Msantd1	C	A	5: 35,075,049 (GRCm39)	T37K	probably benign	Het
Mtus2	A	G	5: 148,243,462 (GRCm39)	E94G	probably damaging	Het
Naaa	A	T	5: 92,407,440 (GRCm39)	L353Q	probably benign	Het
Nek5	T	C	8: 22,610,838 (GRCm39)	E55G	probably benign	Het
Npat	T	C	9: 53,474,749 (GRCm39)	M847T	probably damaging	Het
Nus1	G	A	10: 52,309,539 (GRCm39)	V268I	probably benign	Het
Or51r1	A	G	7: 102,227,801 (GRCm39)	N33S	possibly damaging	Het
Parn	C	T	16: 13,485,428 (GRCm39)	D23N	probably damaging	Het
Pdgfa	T	C	5: 138,964,954 (GRCm39)	E176G	probably damaging	Het
Plcl1	T	A	1: 55,735,405 (GRCm39)	F249I	probably damaging	Het
Plscr5	C	T	9: 92,086,488 (GRCm39)	Q153*	probably null	Het
Polr2b	T	C	5: 77,468,099 (GRCm39)	I133T	probably benign	Het
Polr3c	A	G	3: 96,620,930 (GRCm39)	S463P	probably damaging	Het
Pprc1	A	T	19: 46,060,171 (GRCm39)	I1530L	probably damaging	Het
Prex1	C	T	2: 166,423,904 (GRCm39)	S996N	probably damaging	Het
Rnf169	C	A	7: 99,576,330 (GRCm39)	R291S	possibly damaging	Het
Setd5	A	G	6: 113,087,480 (GRCm39)	K127R	probably damaging	Het
Slc25a26	G	T	6: 94,487,807 (GRCm39)	V89L	probably benign	Het
Slc4a10	A	G	2: 61,877,034 (GRCm39)	T16A	probably benign	Het
Smchd1	A	T	17: 71,747,951 (GRCm39)	H430Q	probably damaging	Het
Ttll7	A	T	3: 146,640,290 (GRCm39)	D503V	probably damaging	Het
Vav2	A	T	2: 27,161,912 (GRCm39)		probably null	Het
Zbtb47	T	C	9: 121,591,937 (GRCm39)	S86P	possibly damaging	Het
Zfp345	A	T	2: 150,314,437 (GRCm39)	C367S	probably damaging	Het
Zfp964	T	A	8: 70,116,106 (GRCm39)	H235Q	possibly damaging	Het

Other mutations in Crlf1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02878:Crlf1	APN	8	70,956,290 (GRCm39)	critical splice donor site	probably null
R0317:Crlf1	UTSW	8	70,951,249 (GRCm39)	missense	probably benign
R0398:Crlf1	UTSW	8	70,951,739 (GRCm39)	splice site	probably benign
R0437:Crlf1	UTSW	8	70,952,164 (GRCm39)	splice site	probably null
R1191:Crlf1	UTSW	8	70,951,478 (GRCm39)	missense	probably damaging	1.00
R1741:Crlf1	UTSW	8	70,953,556 (GRCm39)	missense	probably damaging	0.99
R3730:Crlf1	UTSW	8	70,952,092 (GRCm39)	missense	probably benign	0.03
R3731:Crlf1	UTSW	8	70,952,092 (GRCm39)	missense	probably benign	0.03
R4467:Crlf1	UTSW	8	70,953,606 (GRCm39)	nonsense	probably null
R5557:Crlf1	UTSW	8	70,951,317 (GRCm39)	missense	probably benign	0.12
R6348:Crlf1	UTSW	8	70,945,990 (GRCm39)	missense	probably benign
R6606:Crlf1	UTSW	8	70,953,824 (GRCm39)	missense	probably damaging	1.00
R7947:Crlf1	UTSW	8	70,951,862 (GRCm39)	missense	probably damaging	1.00
R9313:Crlf1	UTSW	8	70,951,466 (GRCm39)	missense	probably damaging	1.00
R9348:Crlf1	UTSW	8	70,951,316 (GRCm39)	missense	probably benign	0.21
X0062:Crlf1	UTSW	8	70,951,487 (GRCm39)	splice site	probably null

Predicted Primers

PCR Primer
(F):5'- CATTCTCTTTAGAGCGCCCG -3'
(R):5'- GGAAAGGGCCTCATCTAGAC -3'

Sequencing Primer
(F):5'- GCTGGCTCAAGAAGCAC -3'
(R):5'- AAAGGGCCTCATCTAGACTGCTG -3'

Posted On

2017-06-26