Mutagenetix > Incidental Mutation

Incidental Mutation 'R8988:Eef1d'

684255

Institutional Source

Beutler Lab

Gene Symbol

Eef1d

Ensembl Gene

ENSMUSG00000055762

Gene Name

eukaryotic translation elongation factor 1 delta

Synonyms

1700026P12Rik, 5730529A16Rik

MMRRC Submission

068820-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.253) question?

Stock #

R8988 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

75766643-75781425 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 75768160 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 561 (Y561H)

Ref Sequence

ENSEMBL: ENSMUSP00000087110 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023235] [ENSMUST00000023237] [ENSMUST00000089680] [ENSMUST00000089681] [ENSMUST00000109972] [ENSMUST00000109975] [ENSMUST00000116440] [ENSMUST00000123712] [ENSMUST00000137426] [ENSMUST00000141268] [ENSMUST00000144614] [ENSMUST00000151066] [ENSMUST00000154584] [ENSMUST00000229571]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000023235
AA Change: Y182H

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000023235
Gene: ENSMUSG00000055762
AA Change: Y182H

Domain	Start	End	E-Value	Type
low complexity region	62	75	N/A	INTRINSIC
coiled coil region	82	120	N/A	INTRINSIC
EF-1_beta_acid	159	186	2.53e-4	SMART
Pfam:EF1_GNE	195	245	3.3e-19	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000023237

SMART Domains

Protein: ENSMUSP00000023237
Gene: ENSMUSG00000022574

Domain	Start	End	E-Value	Type
PDB:4MZY\|A	16	522	2e-70	PDB

Predicted Effect

SMART Domains

Protein: ENSMUSP00000087109
Gene: ENSMUSG00000055762
AA Change: Y177H

Domain	Start	End	E-Value	Type
low complexity region	54	70	N/A	INTRINSIC
coiled coil region	77	115	N/A	INTRINSIC
EF-1_beta_acid	154	181	2.53e-4	SMART
EF1_GNE	190	276	4.87e-41	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000089681
AA Change: Y561H

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

SMART Domains

Protein: ENSMUSP00000087110
Gene: ENSMUSG00000055762
AA Change: Y561H

Domain	Start	End	E-Value	Type
low complexity region	32	52	N/A	INTRINSIC
low complexity region	66	76	N/A	INTRINSIC
internal_repeat_2	108	136	2.92e-5	PROSPERO
low complexity region	137	156	N/A	INTRINSIC
internal_repeat_2	231	259	2.92e-5	PROSPERO
internal_repeat_1	244	263	2.02e-6	PROSPERO
internal_repeat_1	389	408	2.02e-6	PROSPERO
low complexity region	441	454	N/A	INTRINSIC
coiled coil region	461	499	N/A	INTRINSIC
EF-1_beta_acid	538	565	2.53e-4	SMART
EF1_GNE	574	660	4.87e-41	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000109972
AA Change: Y158H

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

SMART Domains

Protein: ENSMUSP00000105599
Gene: ENSMUSG00000055762
AA Change: Y158H

Domain	Start	End	E-Value	Type
low complexity region	35	51	N/A	INTRINSIC
coiled coil region	58	96	N/A	INTRINSIC
EF-1_beta_acid	135	162	2.53e-4	SMART
EF1_GNE	171	257	4.87e-41	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000109975
AA Change: Y561H

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

SMART Domains

Protein: ENSMUSP00000105602
Gene: ENSMUSG00000055762
AA Change: Y561H

Domain	Start	End	E-Value	Type
low complexity region	32	52	N/A	INTRINSIC
low complexity region	66	76	N/A	INTRINSIC
internal_repeat_2	108	136	2.92e-5	PROSPERO
low complexity region	137	156	N/A	INTRINSIC
internal_repeat_2	231	259	2.92e-5	PROSPERO
internal_repeat_1	244	263	2.02e-6	PROSPERO
internal_repeat_1	389	408	2.02e-6	PROSPERO
low complexity region	441	454	N/A	INTRINSIC
coiled coil region	461	499	N/A	INTRINSIC
EF-1_beta_acid	538	565	2.53e-4	SMART
EF1_GNE	574	660	4.87e-41	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000116440
AA Change: Y158H

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

SMART Domains

Protein: ENSMUSP00000112141
Gene: ENSMUSG00000055762
AA Change: Y158H

Domain	Start	End	E-Value	Type
low complexity region	35	51	N/A	INTRINSIC
coiled coil region	58	96	N/A	INTRINSIC
EF-1_beta_acid	135	162	2.53e-4	SMART
EF1_GNE	171	257	4.87e-41	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000123712

SMART Domains

Protein: ENSMUSP00000122155
Gene: ENSMUSG00000055762

Domain	Start	End	E-Value	Type
low complexity region	35	51	N/A	INTRINSIC
coiled coil region	58	96	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000137426
AA Change: Y453H

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

SMART Domains

Protein: ENSMUSP00000114753
Gene: ENSMUSG00000055762
AA Change: Y453H

Domain	Start	End	E-Value	Type
low complexity region	53	72	N/A	INTRINSIC
internal_repeat_1	160	179	9.48e-6	PROSPERO
internal_repeat_1	305	324	9.48e-6	PROSPERO
low complexity region	330	346	N/A	INTRINSIC
coiled coil region	353	391	N/A	INTRINSIC
EF-1_beta_acid	430	457	2.53e-4	SMART
EF1_GNE	466	552	4.87e-41	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000141268
AA Change: Y201H

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

SMART Domains

Protein: ENSMUSP00000115553
Gene: ENSMUSG00000055762
AA Change: Y201H

Domain	Start	End	E-Value	Type
low complexity region	78	94	N/A	INTRINSIC
coiled coil region	101	139	N/A	INTRINSIC
EF-1_beta_acid	178	205	2.53e-4	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000144614
AA Change: Y182H

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000123005
Gene: ENSMUSG00000055762
AA Change: Y182H

Domain	Start	End	E-Value	Type
low complexity region	62	75	N/A	INTRINSIC
coiled coil region	82	120	N/A	INTRINSIC
EF-1_beta_acid	159	186	2.53e-4	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000151066
AA Change: Y91H

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000118889
Gene: ENSMUSG00000055762
AA Change: Y91H

Domain	Start	End	E-Value	Type
EF-1_beta_acid	68	95	2.53e-4	SMART
EF1_GNE	104	190	4.87e-41	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000154584
AA Change: Y182H

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

SMART Domains

Protein: ENSMUSP00000116360
Gene: ENSMUSG00000055762
AA Change: Y182H

Domain	Start	End	E-Value	Type
low complexity region	62	75	N/A	INTRINSIC
coiled coil region	82	120	N/A	INTRINSIC
EF-1_beta_acid	159	186	1.2e-8	SMART
EF1_GNE	195	280	4.9e-41	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000229571

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.3%

Validation Efficiency

96% (81/84)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a subunit of the elongation factor-1 complex, which is responsible for the enzymatic delivery of aminoacyl tRNAs to the ribosome. This subunit, delta, functions as guanine nucleotide exchange factor. It is reported that following HIV-1 infection, this subunit interacts with HIV-1 Tat. This interaction results in repression of translation of host cell proteins and enhanced translation of viral proteins. Several alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. Related pseudogenes have been defined on chromosomes 1, 6, 7, 9, 11, 13, 17, 19.[provided by RefSeq, Aug 2010]

Allele List at MGI

Other mutations in this stock

Total: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abi2	C	T	1: 60,489,251 (GRCm39)	T291I	probably benign	Het
Aox1	A	C	1: 58,088,625 (GRCm39)	D137A	possibly damaging	Het
Apbb2	T	C	5: 66,609,444 (GRCm39)	K68E	probably damaging	Het
Arf3	A	T	15: 98,638,933 (GRCm39)	M108K	probably benign	Het
Atg2b	T	A	12: 105,583,388 (GRCm39)	I2058F	probably damaging	Het
Bhlhe40	C	T	6: 108,639,518 (GRCm39)	L99F	probably damaging	Het
Cd200l1	T	C	16: 45,238,271 (GRCm39)	H294R	probably benign	Het
Cyp2b10	G	A	7: 25,625,670 (GRCm39)	R500H	probably damaging	Het
Dlc1	C	T	8: 37,039,997 (GRCm39)	E937K	probably damaging	Het
Dll3	A	T	7: 27,995,793 (GRCm39)	V336D	possibly damaging	Het
Dync2h1	A	G	9: 7,037,727 (GRCm39)	F3377L	probably benign	Het
Efcab3	T	G	11: 104,911,352 (GRCm39)	V4544G	probably benign	Het
Epb41l1	C	A	2: 156,363,591 (GRCm39)	T700K	probably benign	Het
Epha8	G	T	4: 136,665,897 (GRCm39)	L420M	probably damaging	Het
Ephb2	C	A	4: 136,402,769 (GRCm39)	G501C	probably benign	Het
Erbb3	T	C	10: 128,406,030 (GRCm39)	Y1129C	probably damaging	Het
Fbn1	C	T	2: 125,212,726 (GRCm39)	V799M	possibly damaging	Het
Fbxo9	G	A	9: 77,991,933 (GRCm39)	P353S	probably benign	Het
Ggt1	T	G	10: 75,412,056 (GRCm39)	V100G	probably benign	Het
Gm45861	T	C	8: 28,032,531 (GRCm39)	M885T	unknown	Het
Grin2d	A	T	7: 45,483,425 (GRCm39)	Y917*	probably null	Het
Hectd4	T	A	5: 121,415,819 (GRCm39)	V540D	possibly damaging	Het
Helz	T	A	11: 107,495,079 (GRCm39)	I351K	probably damaging	Het
Ighv2-6-8	A	G	12: 113,759,980 (GRCm39)	V43A	probably damaging	Het
Igkv9-129	T	A	6: 67,817,106 (GRCm39)	I70N	probably damaging	Het
Il18	A	T	9: 50,489,178 (GRCm39)	D69V	probably damaging	Het
Kcnh7	T	A	2: 62,552,209 (GRCm39)	E927D		Het
Kcnt2	T	A	1: 140,356,587 (GRCm39)	V342E	probably benign	Het
Khdc4	A	G	3: 88,607,286 (GRCm39)	N330S	probably benign	Het
Krt1	AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC	AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC	15: 101,758,813 (GRCm39)		probably benign	Het
Krt18	C	G	15: 101,937,962 (GRCm39)	A153G	probably damaging	Het
Lmntd2	A	T	7: 140,791,977 (GRCm39)		probably benign	Het
Lrrc26	G	T	2: 25,180,286 (GRCm39)	A96S	probably benign	Het
Map3k11	A	T	19: 5,752,166 (GRCm39)	S783C	probably damaging	Het
Mib2	G	A	4: 155,740,729 (GRCm39)	L632F	possibly damaging	Het
Mical2	A	C	7: 111,910,661 (GRCm39)	D277A	possibly damaging	Het
Mtr	A	T	13: 12,250,365 (GRCm39)	F339L	probably benign	Het
Musk	T	C	4: 58,354,032 (GRCm39)	F362L	probably benign	Het
Ncor1	G	A	11: 62,233,871 (GRCm39)	Q444*	probably null	Het
Nek4	T	C	14: 30,685,924 (GRCm39)	S279P		Het
Nell1	C	T	7: 50,210,543 (GRCm39)	T348I	unknown	Het
Nicn1	C	T	9: 108,171,708 (GRCm39)	R163C	possibly damaging	Het
Nrip1	T	C	16: 76,088,902 (GRCm39)	H885R	probably damaging	Het
Or13a19	G	A	7: 139,902,938 (GRCm39)	G109R	possibly damaging	Het
Or2a5	T	A	6: 42,874,201 (GRCm39)	V272D		Het
Or2y12	C	A	11: 49,426,028 (GRCm39)	N5K	probably damaging	Het
Or6c208	T	C	10: 129,224,240 (GRCm39)	V246A	probably damaging	Het
Or6c69c	T	A	10: 129,910,522 (GRCm39)	V81D	possibly damaging	Het
Or6d14	A	G	6: 116,534,255 (GRCm39)	T290A	possibly damaging	Het
Otog	A	G	7: 45,959,571 (GRCm39)	D720G	probably damaging	Het
P3h3	C	A	6: 124,834,564 (GRCm39)	Q29H	possibly damaging	Het
Parn	A	G	16: 13,466,281 (GRCm39)		probably null	Het
Pcnt	C	A	10: 76,245,407 (GRCm39)	E1077*	probably null	Het
Peg10	CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG	CCACATCAGGATCCACATCAGGATGCACATCAG	6: 4,756,398 (GRCm39)		probably benign	Het
Pigb	A	G	9: 72,929,576 (GRCm39)	W336R	probably damaging	Het
Pkdrej	A	T	15: 85,700,538 (GRCm39)	S1799R	probably damaging	Het
Pnpla6	G	T	8: 3,567,401 (GRCm39)	M86I	possibly damaging	Het
Prickle2	T	C	6: 92,435,620 (GRCm39)	K50E	possibly damaging	Het
Psg21	A	G	7: 18,386,389 (GRCm39)	V199A	probably benign	Het
Reep3	T	C	10: 66,871,786 (GRCm39)		probably null	Het
Reln	T	C	5: 22,104,155 (GRCm39)	D3272G	probably damaging	Het
Rps6ka4	A	G	19: 6,808,667 (GRCm39)	V526A	possibly damaging	Het
Sel1l3	T	C	5: 53,280,771 (GRCm39)	E911G	probably damaging	Het
Serpinb6b	C	A	13: 33,162,125 (GRCm39)	A308E	probably benign	Het
Slc26a4	A	G	12: 31,572,523 (GRCm39)	V746A	probably benign	Het
Slc4a3	T	G	1: 75,527,957 (GRCm39)	M402R	probably damaging	Het
Slc9b1	A	T	3: 135,078,900 (GRCm39)	T186S	possibly damaging	Het
Slk	A	G	19: 47,608,712 (GRCm39)	Q555R	probably benign	Het
Smc2	T	A	4: 52,475,100 (GRCm39)	D925E	probably benign	Het
Stat5a	A	T	11: 100,774,764 (GRCm39)	T758S	unknown	Het
Sulf1	A	G	1: 12,906,499 (GRCm39)	S514G	probably benign	Het
Tcp11l1	T	A	2: 104,536,853 (GRCm39)	N4I	probably damaging	Het
Tex2	A	T	11: 106,402,731 (GRCm39)	I1047K	unknown	Het
Tmem184b	A	G	15: 79,261,264 (GRCm39)	V114A	possibly damaging	Het
Trmt11	A	G	10: 30,467,027 (GRCm39)	V95A	probably benign	Het
Trp53bp2	A	G	1: 182,268,433 (GRCm39)	D169G	possibly damaging	Het
Ttc41	T	A	10: 86,549,599 (GRCm39)	N264K	possibly damaging	Het
Uba2	A	C	7: 33,853,987 (GRCm39)	S318R	probably benign	Het
Wapl	T	A	14: 34,451,139 (GRCm39)	N724K	probably damaging	Het
Wfdc9	T	A	2: 164,493,671 (GRCm39)	I5F	probably damaging	Het
Zan	C	T	5: 137,406,563 (GRCm39)	D3686N	unknown	Het
Zfp618	A	T	4: 63,012,708 (GRCm39)	Y140F	probably benign	Het
Zfp790	A	G	7: 29,527,593 (GRCm39)	T93A	probably benign	Het
Zfp979	A	C	4: 147,697,984 (GRCm39)	F242V	probably benign	Het

Other mutations in Eef1d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02066:Eef1d	APN	15	75,768,704 (GRCm39)	missense	probably benign	0.10
IGL02265:Eef1d	APN	15	75,775,283 (GRCm39)	missense	probably benign	0.00
IGL02609:Eef1d	APN	15	75,768,162 (GRCm39)	missense	probably null	1.00
IGL02671:Eef1d	APN	15	75,767,654 (GRCm39)	missense	probably damaging	1.00
IGL02728:Eef1d	APN	15	75,774,945 (GRCm39)	missense	probably damaging	1.00
PIT4131001:Eef1d	UTSW	15	75,775,581 (GRCm39)	missense	probably benign	0.01
R0034:Eef1d	UTSW	15	75,774,808 (GRCm39)	missense	probably benign
R0523:Eef1d	UTSW	15	75,775,005 (GRCm39)	missense	probably benign
R0831:Eef1d	UTSW	15	75,768,655 (GRCm39)	unclassified	probably benign
R1164:Eef1d	UTSW	15	75,774,526 (GRCm39)	critical splice donor site	probably null
R1467:Eef1d	UTSW	15	75,767,770 (GRCm39)	missense	probably damaging	1.00
R1467:Eef1d	UTSW	15	75,767,770 (GRCm39)	missense	probably damaging	1.00
R1594:Eef1d	UTSW	15	75,768,195 (GRCm39)	missense	probably damaging	1.00
R1796:Eef1d	UTSW	15	75,773,024 (GRCm39)	missense	probably damaging	1.00
R2039:Eef1d	UTSW	15	75,767,618 (GRCm39)	missense	probably damaging	1.00
R2093:Eef1d	UTSW	15	75,774,550 (GRCm39)	missense	probably benign	0.00
R2119:Eef1d	UTSW	15	75,775,062 (GRCm39)	missense	probably benign	0.43
R2372:Eef1d	UTSW	15	75,768,166 (GRCm39)	missense	probably damaging	1.00
R4401:Eef1d	UTSW	15	75,774,769 (GRCm39)	missense	probably benign
R4403:Eef1d	UTSW	15	75,774,769 (GRCm39)	missense	probably benign
R4425:Eef1d	UTSW	15	75,774,648 (GRCm39)	missense	possibly damaging	0.92
R4614:Eef1d	UTSW	15	75,775,425 (GRCm39)	missense	probably benign	0.00
R4791:Eef1d	UTSW	15	75,775,531 (GRCm39)	missense	possibly damaging	0.85
R4864:Eef1d	UTSW	15	75,775,255 (GRCm39)	missense	possibly damaging	0.73
R5376:Eef1d	UTSW	15	75,775,038 (GRCm39)	missense	probably benign	0.25
R5377:Eef1d	UTSW	15	75,775,038 (GRCm39)	missense	probably benign	0.25
R5415:Eef1d	UTSW	15	75,775,030 (GRCm39)	missense	probably benign	0.00
R6966:Eef1d	UTSW	15	75,775,558 (GRCm39)	missense	probably benign	0.06
R7640:Eef1d	UTSW	15	75,774,556 (GRCm39)	missense	probably damaging	1.00
R8210:Eef1d	UTSW	15	75,768,309 (GRCm39)	missense	probably damaging	1.00
R9316:Eef1d	UTSW	15	75,781,130 (GRCm39)	unclassified	probably benign
Z1177:Eef1d	UTSW	15	75,774,727 (GRCm39)	missense	possibly damaging	0.91

Predicted Primers

PCR Primer
(F):5'- AGTCCCAGGTTTACATGCCTC -3'
(R):5'- GATGAGTCTCAGCCTTCCTC -3'

Sequencing Primer
(F):5'- AGGTTTACATGCCTCACTCCAC -3'
(R):5'- CCCTCCCTCTGTGGCAG -3'

Posted On

2021-10-11