Mutagenetix > Incidental Mutation

Incidental Mutation 'R5256:Dlk1'

399701

Institutional Source

Beutler Lab

Gene Symbol

Dlk1

Ensembl Gene

ENSMUSG00000040856

Gene Name

delta like non-canonical Notch ligand 1

Synonyms

SCP1, pref-1, pG2, Peg9, ZOG, DlkI, FA1

MMRRC Submission

042827-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.657) question?

Stock #

R5256 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

109418749-109429262 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 109425697 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 190 (I190N)

Ref Sequence

ENSEMBL: ENSMUSP00000105472 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056110] [ENSMUST00000109841] [ENSMUST00000109842] [ENSMUST00000109843] [ENSMUST00000109844] [ENSMUST00000109846] [ENSMUST00000124293] [ENSMUST00000173539]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000056110
AA Change: I190N

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

SMART Domains

Protein: ENSMUSP00000063104
Gene: ENSMUSG00000040856
AA Change: I190N

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
EGF	25	55	1.43e-1	SMART
EGF	56	86	1.26e-2	SMART
EGF_CA	88	125	1.77e-6	SMART
EGF	130	168	8.71e-6	SMART
EGF	175	208	1.41e-5	SMART
EGF	213	247	4.06e-6	SMART
transmembrane domain	307	329	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000109841
AA Change: I190N

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

SMART Domains

Protein: ENSMUSP00000105467
Gene: ENSMUSG00000040856
AA Change: I190N

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
EGF	25	55	1.43e-1	SMART
EGF	56	86	1.26e-2	SMART
EGF_CA	88	125	1.77e-6	SMART
EGF	130	168	8.71e-6	SMART
EGF	175	208	1.41e-5	SMART
transmembrane domain	214	236	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000109842
AA Change: I190N

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

SMART Domains

Protein: ENSMUSP00000105468
Gene: ENSMUSG00000040856
AA Change: I190N

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
EGF	25	55	1.43e-1	SMART
EGF	56	86	1.26e-2	SMART
EGF_CA	88	125	1.77e-6	SMART
EGF	130	168	8.71e-6	SMART
EGF	175	208	1.41e-5	SMART
transmembrane domain	234	256	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000109843
AA Change: I190N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000105469
Gene: ENSMUSG00000040856
AA Change: I190N

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
EGF	25	55	1.43e-1	SMART
EGF	56	86	1.26e-2	SMART
EGF_CA	88	125	1.77e-6	SMART
EGF	130	168	8.71e-6	SMART
EGF	175	208	1.41e-5	SMART
transmembrane domain	212	234	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000109844
AA Change: I190N

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

SMART Domains

Protein: ENSMUSP00000105470
Gene: ENSMUSG00000040856
AA Change: I190N

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
EGF	25	55	1.43e-1	SMART
EGF	56	86	1.26e-2	SMART
EGF_CA	88	125	1.77e-6	SMART
EGF	130	168	8.71e-6	SMART
EGF	175	208	1.41e-5	SMART
EGF	213	247	4.06e-6	SMART
transmembrane domain	307	329	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000109846
AA Change: I190N

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

SMART Domains

Protein: ENSMUSP00000105472
Gene: ENSMUSG00000040856
AA Change: I190N

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
EGF	25	55	1.43e-1	SMART
EGF	56	86	1.26e-2	SMART
EGF_CA	88	125	1.77e-6	SMART
EGF	130	168	8.71e-6	SMART
EGF	175	208	1.41e-5	SMART
transmembrane domain	256	278	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000124293

SMART Domains

Protein: ENSMUSP00000133530
Gene: ENSMUSG00000040856

Domain	Start	End	E-Value	Type
EGF	24	54	1.43e-1	SMART
EGF	55	85	1.26e-2	SMART
EGF_CA	87	124	1.77e-6	SMART
EGF	129	167	8.71e-6	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000173539
AA Change: I190N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000133430
Gene: ENSMUSG00000040856
AA Change: I190N

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
EGF	25	55	1.43e-1	SMART
EGF	56	86	1.26e-2	SMART
EGF_CA	88	125	1.77e-6	SMART
EGF	130	168	8.71e-6	SMART
EGF	175	208	1.41e-5	SMART
transmembrane domain	232	254	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000173812

SMART Domains

Protein: ENSMUSP00000134308
Gene: ENSMUSG00000040856

Domain	Start	End	E-Value	Type
SCOP:d1eqga2	2	15	4e-3	SMART
transmembrane domain	44	66	N/A	INTRINSIC

Meta Mutation Damage Score

0.1508

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.4%
20x: 92.8%

Validation Efficiency

97% (95/98)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a transmembrane protein that contains multiple epidermal growth factor repeats that functions as a regulator of cell growth. The encoded protein is involved in the differentiation of several cell types including adipocytes. This gene is located in a region of chromosome 14 frequently showing unparental disomy, and is imprinted and expressed from the paternal allele. A single nucleotide variant in this gene is associated with child and adolescent obesity and shows polar overdominance, where heterozygotes carrying an active paternal allele express the phenotype, while mutant homozygotes are normal. [provided by RefSeq, Nov 2015]
PHENOTYPE: Homozygote null mice have reduced fetal growth and 50% lethality 2 days after birth. Survivors are small but have enlarged fat pad masses. Homozygotes for another null allele have abnormal B cell development. Paternally-inherited null alleles phenocopy homozygotes due to maternal imprinting. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A730015C16Rik	C	A	4: 108,705,262 (GRCm39)		probably benign	Het
Actr1b	T	C	1: 36,739,173 (GRCm39)	H372R	probably benign	Het
Ampd2	C	A	3: 107,986,865 (GRCm39)		probably benign	Het
Anapc4	A	G	5: 53,020,936 (GRCm39)	S612G	probably benign	Het
Arhgef7	T	C	8: 11,850,811 (GRCm39)	L141P	probably damaging	Het
Atl1	A	G	12: 70,006,107 (GRCm39)	D471G	probably damaging	Het
Atrn	A	G	2: 130,787,939 (GRCm39)	D247G	probably benign	Het
Bag1	T	A	4: 40,948,022 (GRCm39)	R61W	probably damaging	Het
Card10	C	T	15: 78,662,451 (GRCm39)	R898H	probably damaging	Het
Cct6b	G	A	11: 82,655,046 (GRCm39)	A3V	probably damaging	Het
Cfap54	A	T	10: 92,770,953 (GRCm39)	L2097*	probably null	Het
Cfap54	T	C	10: 92,880,885 (GRCm39)		probably null	Het
Chd5	T	C	4: 152,456,554 (GRCm39)	F964L	probably benign	Het
Cog5	A	G	12: 31,936,204 (GRCm39)	T584A	probably benign	Het
Cpa2	T	A	6: 30,547,196 (GRCm39)	N157K	probably damaging	Het
Cpeb1	A	T	7: 81,001,587 (GRCm39)	M440K	probably damaging	Het
Cracr2a	G	A	6: 127,580,992 (GRCm39)	C56Y	probably damaging	Het
Ddb2	A	C	2: 91,067,073 (GRCm39)	L30R	probably damaging	Het
Dnaaf4	T	C	9: 72,879,362 (GRCm39)		probably null	Het
Dnajc13	T	A	9: 104,080,528 (GRCm39)	Y851F	possibly damaging	Het
Dop1a	T	A	9: 86,397,381 (GRCm39)	L895Q	probably damaging	Het
F7	G	A	8: 13,080,763 (GRCm39)	C122Y	probably damaging	Het
Frrs1	T	C	3: 116,696,749 (GRCm39)	V573A	possibly damaging	Het
Galnt2l	T	C	8: 122,997,175 (GRCm39)		probably benign	Het
Gm17541	A	T	12: 4,739,672 (GRCm39)		probably benign	Het
Gm5519	A	T	19: 33,800,576 (GRCm39)	H90L	probably damaging	Het
Gm5526	T	A	1: 45,896,569 (GRCm39)		noncoding transcript	Het
Gm5709	A	T	3: 59,509,971 (GRCm39)		noncoding transcript	Het
Golga4	T	A	9: 118,385,569 (GRCm39)	V869D	possibly damaging	Het
Grm7	A	T	6: 111,335,182 (GRCm39)	Q531L	probably benign	Het
Hnrnpu	C	A	1: 178,163,458 (GRCm39)	C265F	unknown	Het
Hoxd3	G	A	2: 74,577,211 (GRCm39)	V364I	possibly damaging	Het
Hspb8	T	C	5: 116,547,532 (GRCm39)	D150G	probably damaging	Het
Hydin	C	A	8: 111,313,855 (GRCm39)	N4244K	possibly damaging	Het
Ik	A	G	18: 36,881,926 (GRCm39)	D136G	probably benign	Het
Il11ra1	T	C	4: 41,767,932 (GRCm39)		probably benign	Het
Jph1	T	C	1: 17,161,622 (GRCm39)	I347V	probably benign	Het
Klk1	T	A	7: 43,870,985 (GRCm39)		probably benign	Het
Lmcd1	T	A	6: 112,265,087 (GRCm39)		probably benign	Het
Lnx1	C	T	5: 74,846,315 (GRCm39)	C45Y	probably damaging	Het
Macc1	T	A	12: 119,410,264 (GRCm39)	M344K	possibly damaging	Het
Madcam1	A	G	10: 79,500,779 (GRCm39)	E32G	possibly damaging	Het
Mat2a	T	C	6: 72,411,316 (GRCm39)	D383G	probably benign	Het
Mpst	T	A	15: 78,297,849 (GRCm39)	I289N	probably damaging	Het
Myh6	C	T	14: 55,190,118 (GRCm39)	R1055Q	probably damaging	Het
Myh7	T	C	14: 55,216,965 (GRCm39)	K1131E	probably damaging	Het
Ndrg3	A	T	2: 156,773,125 (GRCm39)		probably benign	Het
Nebl	A	G	2: 17,438,786 (GRCm39)	S209P	probably benign	Het
Nid2	A	G	14: 19,818,276 (GRCm39)		probably null	Het
Nup188	A	T	2: 30,220,761 (GRCm39)	S945C	probably damaging	Het
Or1j21	A	G	2: 36,683,685 (GRCm39)	M146V	probably benign	Het
Or5g23	C	T	2: 85,438,817 (GRCm39)	V146I	probably benign	Het
Or8c11	A	G	9: 38,289,213 (GRCm39)	N12S	probably benign	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
Patl2	A	G	2: 121,959,368 (GRCm39)	L32P	probably damaging	Het
Pcdh20	T	A	14: 88,705,813 (GRCm39)	M496L	probably benign	Het
Pdzd2	A	G	15: 12,373,028 (GRCm39)	V2369A	possibly damaging	Het
Pfn2	A	G	3: 57,754,812 (GRCm39)	V31A	probably damaging	Het
Plxna4	T	C	6: 32,228,007 (GRCm39)	N533S	probably benign	Het
Plxnb1	T	C	9: 108,943,661 (GRCm39)	F1916S	probably damaging	Het
Ppp4r3b	T	C	11: 29,138,293 (GRCm39)	F214L	probably benign	Het
Prox1	T	C	1: 189,893,638 (GRCm39)	D269G	probably benign	Het
Rapgef4	T	C	2: 71,864,378 (GRCm39)	F71S	probably damaging	Het
Rft1	A	G	14: 30,383,243 (GRCm39)	I94M	probably benign	Het
S100z	T	C	13: 95,615,127 (GRCm39)	I13V	probably damaging	Het
Serhl	T	A	15: 82,986,835 (GRCm39)	V117E	probably damaging	Het
Shroom1	G	A	11: 53,356,334 (GRCm39)	R336Q	probably benign	Het
Sik3	A	T	9: 46,123,552 (GRCm39)	Q1067L	probably damaging	Het
Slc22a30	G	A	19: 8,321,757 (GRCm39)	Q436*	probably null	Het
Slc28a1	G	A	7: 80,771,869 (GRCm39)	V118M	probably damaging	Het
Slco1a6	T	A	6: 142,078,427 (GRCm39)	I153F	probably benign	Het
Ss18l1	T	C	2: 179,703,735 (GRCm39)	Y323H	unknown	Het
Susd4	G	T	1: 182,719,824 (GRCm39)	A480S	possibly damaging	Het
Syne3	A	T	12: 104,942,139 (GRCm39)	M1K	probably null	Het
Synpo2l	A	T	14: 20,711,082 (GRCm39)	S513T	probably benign	Het
Tat	A	T	8: 110,724,966 (GRCm39)	N388I	probably benign	Het
Tbc1d1	A	G	5: 64,439,352 (GRCm39)	Y619C	probably damaging	Het
Tbk1	G	A	10: 121,406,590 (GRCm39)	T216M	probably damaging	Het
Tns1	C	T	1: 74,034,585 (GRCm39)		probably benign	Het
Trbv5	T	C	6: 41,039,318 (GRCm39)	V9A	possibly damaging	Het
Trpm5	A	G	7: 142,636,040 (GRCm39)	Y575H	probably damaging	Het
Ttn	A	T	2: 76,570,045 (GRCm39)	Y25203*	probably null	Het
Tubb3	C	A	8: 124,148,391 (GRCm39)	D441E	probably benign	Het
Usp33	T	A	3: 152,097,333 (GRCm39)	C850*	probably null	Het
Vdac1	G	A	11: 52,274,905 (GRCm39)		probably null	Het
Vmn1r232	T	C	17: 21,133,846 (GRCm39)	I251M	probably damaging	Het
Vmn2r11	T	G	5: 109,202,658 (GRCm39)	I140L	probably benign	Het
Vmn2r6	A	T	3: 64,464,263 (GRCm39)	N190K	probably benign	Het
Vps51	T	A	19: 6,120,518 (GRCm39)	H465L	probably benign	Het
Zfp318	T	G	17: 46,722,995 (GRCm39)	I1666S	probably benign	Het
Zfp446	C	T	7: 12,713,231 (GRCm39)	R90*	probably null	Het
Zgrf1	T	A	3: 127,396,094 (GRCm39)	F547I	probably damaging	Het

Other mutations in Dlk1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0041:Dlk1	UTSW	12	109,421,439 (GRCm39)	missense	probably damaging	1.00
R0379:Dlk1	UTSW	12	109,420,985 (GRCm39)	unclassified	probably benign
R1250:Dlk1	UTSW	12	109,425,744 (GRCm39)	missense	probably damaging	1.00
R1363:Dlk1	UTSW	12	109,421,430 (GRCm39)	missense	probably damaging	1.00
R1757:Dlk1	UTSW	12	109,425,613 (GRCm39)	missense	probably damaging	1.00
R1763:Dlk1	UTSW	12	109,424,045 (GRCm39)	missense	probably damaging	1.00
R1772:Dlk1	UTSW	12	109,425,685 (GRCm39)	missense	probably damaging	1.00
R2189:Dlk1	UTSW	12	109,420,975 (GRCm39)	critical splice donor site	probably null
R2334:Dlk1	UTSW	12	109,419,614 (GRCm39)	missense	probably damaging	0.96
R3751:Dlk1	UTSW	12	109,426,239 (GRCm39)	missense	probably benign	0.15
R5268:Dlk1	UTSW	12	109,425,764 (GRCm39)	missense	probably benign	0.34
R5356:Dlk1	UTSW	12	109,421,447 (GRCm39)	missense	probably damaging	0.99
R5669:Dlk1	UTSW	12	109,425,964 (GRCm39)	missense	probably benign	0.04
R5748:Dlk1	UTSW	12	109,425,898 (GRCm39)	missense	probably benign	0.00
R5992:Dlk1	UTSW	12	109,421,507 (GRCm39)	missense	probably damaging	1.00
R6076:Dlk1	UTSW	12	109,425,895 (GRCm39)	missense	probably damaging	0.98
R6539:Dlk1	UTSW	12	109,426,245 (GRCm39)	missense	probably benign	0.01
R6638:Dlk1	UTSW	12	109,426,204 (GRCm39)	missense	probably damaging	1.00
R7480:Dlk1	UTSW	12	109,421,540 (GRCm39)	missense	probably damaging	1.00
R7553:Dlk1	UTSW	12	109,420,889 (GRCm39)	missense	unknown
R7602:Dlk1	UTSW	12	109,421,551 (GRCm39)	critical splice donor site	probably null
R8531:Dlk1	UTSW	12	109,424,066 (GRCm39)	missense	probably null	0.06
R9120:Dlk1	UTSW	12	109,424,051 (GRCm39)	missense	probably benign	0.00
R9554:Dlk1	UTSW	12	109,420,889 (GRCm39)	missense	unknown
X0020:Dlk1	UTSW	12	109,425,838 (GRCm39)	missense	probably damaging	1.00
X0053:Dlk1	UTSW	12	109,426,063 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GTTACAGTTCTCCCTGCCAG -3'
(R):5'- ACCTTCAGGATGTGTTGCTC -3'

Sequencing Primer
(F):5'- TTCTCCCTGCCAGCACGG -3'
(R):5'- TGAACAGGCAGCTCGTG -3'

Posted On

2016-07-06