Mutagenetix > Incidental Mutation

Incidental Mutation 'R4896:Hmgcll1'

377655

Institutional Source

Beutler Lab

Gene Symbol

Hmgcll1

Ensembl Gene

ENSMUSG00000007908

Gene Name

3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1

Synonyms

MMRRC Submission

042500-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.073) question?

Stock #

R4896 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

75922137-76043632 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 75963460 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Phenylalanine at position 39 (S39F)

Ref Sequence

ENSEMBL: ENSMUSP00000139094 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000008052] [ENSMUST00000117981] [ENSMUST00000183425] [ENSMUST00000183979]

AlphaFold

Q8JZS7

Predicted Effect

probably benign
Transcript: ENSMUST00000008052
AA Change: S39F

PolyPhen 2 Score 0.100 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000008052
Gene: ENSMUSG00000007908
AA Change: S39F

Domain	Start	End	E-Value	Type
Pfam:HMGL-like	47	321	2.2e-67	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000117981
AA Change: S39F

PolyPhen 2 Score 0.300 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000114045
Gene: ENSMUSG00000007908
AA Change: S39F

Domain	Start	End	E-Value	Type
Pfam:HMGL-like	56	104	1e-10	PFAM
Pfam:HMGL-like	99	183	2e-8	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000121592

SMART Domains

Protein: ENSMUSP00000113290
Gene: ENSMUSG00000007908

Domain	Start	End	E-Value	Type
Pfam:HMGL-like	56	215	8.8e-28	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126321

Predicted Effect

possibly damaging
Transcript: ENSMUST00000183425
AA Change: S39F

PolyPhen 2 Score 0.734 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000139094
Gene: ENSMUSG00000007908
AA Change: S39F

Domain	Start	End	E-Value	Type
Pfam:HMGL-like	56	101	8.5e-11	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000183505

Predicted Effect

possibly damaging
Transcript: ENSMUST00000183979
AA Change: S39F

PolyPhen 2 Score 0.699 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000138914
Gene: ENSMUSG00000007908
AA Change: S39F

Domain	Start	End	E-Value	Type
Pfam:HMGL-like	56	104	6.4e-11	PFAM
Pfam:HMGL-like	98	201	1.6e-32	PFAM

Meta Mutation Damage Score

0.1522

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.5%

Validation Efficiency

99% (101/102)

Allele List at MGI

All alleles(6) : Targeted(2) Gene trapped(4)

Other mutations in this stock

Total: 95 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb4	T	C	5: 8,957,267 (GRCm39)	V132A	possibly damaging	Het
Acp3	A	T	9: 104,184,174 (GRCm39)	V292E	probably damaging	Het
Adamts10	T	C	17: 33,747,870 (GRCm39)	V102A	possibly damaging	Het
Add2	A	G	6: 86,073,728 (GRCm39)	T206A	probably benign	Het
Alg12	A	T	15: 88,700,391 (GRCm39)	L15Q	probably damaging	Het
Ankrd27	T	A	7: 35,307,800 (GRCm39)	D346E	probably damaging	Het
Armc2	A	T	10: 41,799,790 (GRCm39)	N689K	probably damaging	Het
Best3	T	A	10: 116,860,460 (GRCm39)	D573E	probably benign	Het
Bltp1	T	G	3: 37,020,086 (GRCm39)	N2108K	probably damaging	Het
Ccdc80	A	T	16: 44,916,261 (GRCm39)	Q339L	probably benign	Het
Cdh9	T	C	15: 16,778,242 (GRCm39)	V19A	probably benign	Het
Cimap1a	G	A	7: 140,428,398 (GRCm39)		probably benign	Het
Cnksr1	A	T	4: 133,956,986 (GRCm39)		probably null	Het
Col7a1	T	A	9: 108,786,345 (GRCm39)	V525E	unknown	Het
Cplane1	T	C	15: 8,251,421 (GRCm39)	S1898P	probably benign	Het
Crebrf	T	C	17: 26,961,394 (GRCm39)	S172P	possibly damaging	Het
Csmd1	T	C	8: 16,059,439 (GRCm39)	I2099V	probably benign	Het
Dcaf4	T	A	12: 83,586,233 (GRCm39)	M400K	possibly damaging	Het
Dnah11	A	T	12: 117,958,935 (GRCm39)	F2983I	probably damaging	Het
Dock6	A	G	9: 21,735,733 (GRCm39)	V1005A	possibly damaging	Het
Dyrk2	C	A	10: 118,704,153 (GRCm39)	G34C	probably damaging	Het
Eif4a1	A	T	11: 69,559,423 (GRCm39)		probably benign	Het
Eno4	G	T	19: 58,952,975 (GRCm39)	D330Y	probably damaging	Het
Faf1	G	A	4: 109,699,496 (GRCm39)	C347Y	probably benign	Het
Fam169a	A	G	13: 97,234,100 (GRCm39)	Y124C	probably damaging	Het
Fam227a	G	T	15: 79,521,255 (GRCm39)	F269L	probably benign	Het
Fancm	C	A	12: 65,122,605 (GRCm39)	D42E	probably damaging	Het
Fat1	T	A	8: 45,404,317 (GRCm39)	I356N	possibly damaging	Het
Fer1l6	A	T	15: 58,509,869 (GRCm39)	T1444S	probably damaging	Het
Galr1	A	G	18: 82,412,065 (GRCm39)	L267P	probably damaging	Het
Gbx1	T	C	5: 24,709,837 (GRCm39)	H336R	probably damaging	Het
Gimap8	A	T	6: 48,636,281 (GRCm39)	Q682L	possibly damaging	Het
Gm2396	T	G	9: 88,813,281 (GRCm39)		noncoding transcript	Het
Gm5798	T	C	14: 41,070,614 (GRCm39)	L8S	probably damaging	Het
Hspg2	C	T	4: 137,246,251 (GRCm39)	R1010C	probably damaging	Het
Il3ra	A	T	14: 14,355,381 (GRCm38)	E289D	probably benign	Het
Isoc1	T	A	18: 58,806,350 (GRCm39)	L220Q	probably damaging	Het
Itga2	T	A	13: 114,990,302 (GRCm39)	K918*	probably null	Het
Kat6a	C	T	8: 23,428,329 (GRCm39)	T1228I	probably benign	Het
Klhl30	T	A	1: 91,287,046 (GRCm39)		probably null	Het
Krtap6-2	A	T	16: 89,216,806 (GRCm39)	C54S	unknown	Het
Lmf2	G	A	15: 89,236,003 (GRCm39)	P634S	probably benign	Het
Map3k4	A	G	17: 12,490,906 (GRCm39)	V175A	possibly damaging	Het
Mcm3	A	C	1: 20,890,480 (GRCm39)		probably benign	Het
Mon1b	T	C	8: 114,365,859 (GRCm39)	S396P	probably damaging	Het
Mroh2a	T	C	1: 88,184,476 (GRCm39)	V1453A	probably benign	Het
Ncor2	A	G	5: 125,126,404 (GRCm39)		probably null	Het
Nlrc5	T	G	8: 95,247,844 (GRCm39)		probably benign	Het
Nlrp14	GT	GTT	7: 106,796,386 (GRCm39)		probably null	Het
Nwd2	T	G	5: 63,962,151 (GRCm39)	S578R	probably damaging	Het
Or12k7	A	G	2: 36,958,422 (GRCm39)	Y35C	probably damaging	Het
Or4f4b	G	A	2: 111,314,005 (GRCm39)	V105I	possibly damaging	Het
Otoa	C	A	7: 120,701,902 (GRCm39)	P194T	probably damaging	Het
Pde1b	A	C	15: 103,429,801 (GRCm39)	D98A	probably damaging	Het
Pi4ka	A	T	16: 17,195,033 (GRCm39)	C122S	probably damaging	Het
Pole2	C	T	12: 69,269,924 (GRCm39)	V67M	probably damaging	Het
Prickle2	A	T	6: 92,393,736 (GRCm39)	D312E	probably benign	Het
Prkd1	T	C	12: 50,436,745 (GRCm39)	D453G	probably damaging	Het
Prrc1	T	A	18: 57,507,626 (GRCm39)	V260E	probably damaging	Het
Reg3g	A	T	6: 78,444,793 (GRCm39)	Y62N	probably benign	Het
Reln	C	T	5: 22,160,236 (GRCm39)	G2111E	probably damaging	Het
Rsph6a	A	T	7: 18,791,665 (GRCm39)	E278V	possibly damaging	Het
Scpep1	T	A	11: 88,832,122 (GRCm39)	I203F	probably damaging	Het
Sec24d	T	C	3: 123,148,596 (GRCm39)	C747R	probably damaging	Het
Sec31a	A	T	5: 100,516,192 (GRCm39)	N967K	probably damaging	Het
Sell	T	C	1: 163,890,631 (GRCm39)	W5R	probably benign	Het
Siglec1	C	T	2: 130,911,789 (GRCm39)	V1697M	probably benign	Het
Sinhcaf	A	G	6: 148,834,498 (GRCm39)		probably null	Het
Slc22a26	T	A	19: 7,768,419 (GRCm39)	I213L	probably benign	Het
Slc2a13	G	A	15: 91,296,415 (GRCm39)	P300S	probably benign	Het
Slco1a4	A	G	6: 141,761,231 (GRCm39)	Y461H	possibly damaging	Het
Slco3a1	G	C	7: 73,970,304 (GRCm39)	C434W	probably null	Het
Sp3	A	T	2: 72,768,633 (GRCm39)	V666D	probably benign	Het
Spidr	A	T	16: 15,936,806 (GRCm39)	W100R	possibly damaging	Het
Stk33	T	A	7: 108,926,802 (GRCm39)	M286L	probably damaging	Het
Sult1c2	T	A	17: 54,139,163 (GRCm39)	I183F	probably benign	Het
Svep1	G	T	4: 58,087,751 (GRCm39)	T1776K	probably benign	Het
Tesk2	A	G	4: 116,660,190 (GRCm39)	H436R	probably benign	Het
Tex2	T	C	11: 106,459,230 (GRCm39)	T67A	probably damaging	Het
Timm10	T	C	2: 84,660,192 (GRCm39)	S44P	possibly damaging	Het
Tmed11	C	A	5: 108,943,048 (GRCm39)		probably null	Het
Trim12c	G	A	7: 103,990,155 (GRCm39)	R441C	probably damaging	Het
Trmt2a	A	G	16: 18,070,793 (GRCm39)	K509E	probably damaging	Het
Upk3a	A	G	15: 84,903,624 (GRCm39)	T108A	probably benign	Het
Usp29	A	G	7: 6,965,158 (GRCm39)	M334V	probably benign	Het
Vash1	A	G	12: 86,726,916 (GRCm39)	D52G	probably benign	Het
Vmn2r14	T	G	5: 109,368,246 (GRCm39)	T249P	probably benign	Het
Vmn2r43	A	T	7: 8,247,848 (GRCm39)	F772I	probably damaging	Het
Vmn2r75	G	T	7: 85,820,787 (GRCm39)	S49Y	probably benign	Het
Xdh	T	C	17: 74,217,238 (GRCm39)	T677A	probably damaging	Het
Zan	A	G	5: 137,384,718 (GRCm39)	L5102P	unknown	Het
Zfp160	T	A	17: 21,240,343 (GRCm39)	S9T	probably benign	Het
Zfp273	A	T	13: 67,973,673 (GRCm39)	H267L	probably damaging	Het
Zfp97	T	A	17: 17,365,038 (GRCm39)	I179K	probably benign	Het
Zfp975	T	C	7: 42,311,716 (GRCm39)	Y299C	probably damaging	Het

Other mutations in Hmgcll1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02151:Hmgcll1	APN	9	75,988,720 (GRCm39)	missense	probably benign	0.01
mephistopheles	UTSW	9	75,988,731 (GRCm39)	missense	probably benign	0.00
P0005:Hmgcll1	UTSW	9	75,982,041 (GRCm39)	missense	possibly damaging	0.90
R1178:Hmgcll1	UTSW	9	76,037,613 (GRCm39)	missense	probably damaging	1.00
R3907:Hmgcll1	UTSW	9	75,979,943 (GRCm39)	missense	probably benign
R4161:Hmgcll1	UTSW	9	75,982,198 (GRCm39)	intron	probably benign
R4843:Hmgcll1	UTSW	9	75,979,916 (GRCm39)	missense	possibly damaging	0.79
R5614:Hmgcll1	UTSW	9	75,988,675 (GRCm39)	missense	probably damaging	1.00
R5702:Hmgcll1	UTSW	9	75,991,672 (GRCm39)	missense	possibly damaging	0.67
R6272:Hmgcll1	UTSW	9	76,037,627 (GRCm39)	missense	probably damaging	1.00
R6681:Hmgcll1	UTSW	9	75,988,731 (GRCm39)	missense	probably benign	0.00
R7075:Hmgcll1	UTSW	9	75,963,834 (GRCm39)	missense	possibly damaging	0.89
R8097:Hmgcll1	UTSW	9	75,922,421 (GRCm39)	missense	probably benign	0.00
R8987:Hmgcll1	UTSW	9	76,037,592 (GRCm39)	critical splice acceptor site	probably null
R9215:Hmgcll1	UTSW	9	75,982,083 (GRCm39)	missense	probably benign
R9228:Hmgcll1	UTSW	9	75,991,732 (GRCm39)	missense	probably damaging	1.00
R9662:Hmgcll1	UTSW	9	75,922,397 (GRCm39)	missense	probably benign	0.31
X0054:Hmgcll1	UTSW	9	76,037,686 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTCCTCCAACAAGGCTGTGTC -3'
(R):5'- ACAAGCCAGTTTGGGAAAGTTG -3'

Sequencing Primer
(F):5'- AGGCTGTGTCCCTCAAAACTC -3'
(R):5'- CCCAATTGGAAGCAAATACATTATG -3'

Posted On

2016-03-17