Mutagenetix > Incidental Mutation

Incidental Mutation 'R3056:Slc4a4'

265175

Institutional Source

Beutler Lab

Gene Symbol

Slc4a4

Ensembl Gene

ENSMUSG00000060961

Gene Name

solute carrier family 4 (anion exchanger), member 4

Synonyms

NBC, NBC1

MMRRC Submission

040565-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3056 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

89034345-89387512 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 89373807 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 971 (V971A)

Ref Sequence

ENSEMBL: ENSMUSP00000121744 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000113218] [ENSMUST00000130041] [ENSMUST00000148750] [ENSMUST00000156238]

AlphaFold

O88343

Predicted Effect

probably damaging
Transcript: ENSMUST00000113218
AA Change: V962A

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

SMART Domains

Protein: ENSMUSP00000108844
Gene: ENSMUSG00000060961
AA Change: V962A

Domain	Start	End	E-Value	Type
low complexity region	40	59	N/A	INTRINSIC
low complexity region	76	87	N/A	INTRINSIC
Pfam:Band_3_cyto	137	379	1.1e-100	PFAM
low complexity region	408	423	N/A	INTRINSIC
Pfam:HCO3_cotransp	426	947	3e-246	PFAM
transmembrane domain	953	975	N/A	INTRINSIC
low complexity region	999	1015	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000130041
AA Change: V927A

PolyPhen 2 Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000118413
Gene: ENSMUSG00000060961
AA Change: V927A

Domain	Start	End	E-Value	Type
Pfam:Band_3_cyto	93	344	1.5e-101	PFAM
low complexity region	373	388	N/A	INTRINSIC
Pfam:HCO3_cotransp	391	912	2.7e-246	PFAM
transmembrane domain	918	940	N/A	INTRINSIC
low complexity region	964	980	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000148750
AA Change: V971A

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

SMART Domains

Protein: ENSMUSP00000119325
Gene: ENSMUSG00000060961
AA Change: V971A

Domain	Start	End	E-Value	Type
low complexity region	40	59	N/A	INTRINSIC
low complexity region	76	87	N/A	INTRINSIC
Pfam:Band_3_cyto	137	388	3.7e-101	PFAM
low complexity region	417	432	N/A	INTRINSIC
Pfam:HCO3_cotransp	435	956	7.3e-246	PFAM
transmembrane domain	962	984	N/A	INTRINSIC
low complexity region	1008	1024	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000156238
AA Change: V971A

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

SMART Domains

Protein: ENSMUSP00000121744
Gene: ENSMUSG00000060961
AA Change: V971A

Domain	Start	End	E-Value	Type
low complexity region	40	59	N/A	INTRINSIC
low complexity region	76	87	N/A	INTRINSIC
Pfam:Band_3_cyto	137	388	4.6e-101	PFAM
low complexity region	417	432	N/A	INTRINSIC
Pfam:HCO3_cotransp	436	956	4.1e-231	PFAM
transmembrane domain	962	984	N/A	INTRINSIC
low complexity region	1008	1024	N/A	INTRINSIC

Meta Mutation Damage Score

0.0974

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.8%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a sodium bicarbonate cotransporter (NBC) involved in the regulation of bicarbonate secretion and absorption and intracellular pH. Mutations in this gene are associated with proximal renal tubular acidosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
PHENOTYPE: Mice homozygous for a null allele exhibit smaller birth size, growth retardation, postnatal lethality, bowel obstructions, altered blood chemistry, acidosis, spleen defects and defects in ion homeostasis. Heterozygotes have decreased levels of circulating bicarbonate. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 39 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl4fm4	A	G	4: 144,401,268 (GRCm39)	I72T	probably benign	Het
Abca1	A	T	4: 53,127,626 (GRCm39)	M131K	probably benign	Het
Agbl1	C	T	7: 76,416,232 (GRCm39)	T751M	possibly damaging	Het
Asb14	A	G	14: 26,636,146 (GRCm39)	I510V	possibly damaging	Het
Bard1	A	G	1: 71,127,390 (GRCm39)	V73A	possibly damaging	Het
C6	T	C	15: 4,769,355 (GRCm39)	I187T	probably damaging	Het
Catsper3	T	C	13: 55,956,709 (GRCm39)	S376P	unknown	Het
Ccdc150	A	G	1: 54,328,001 (GRCm39)	N361S	possibly damaging	Het
Cntn5	A	G	9: 10,419,076 (GRCm39)	L7P	probably benign	Het
Cplane1	T	C	15: 8,280,491 (GRCm39)	S2805P	unknown	Het
Cxcr6	A	T	9: 123,639,529 (GRCm39)	I177F	probably damaging	Het
Dnah7b	A	G	1: 46,307,869 (GRCm39)	D3061G	possibly damaging	Het
Epas1	T	C	17: 87,138,409 (GRCm39)	F835S	probably damaging	Het
Fat3	C	T	9: 15,871,792 (GRCm39)	R3533H	probably benign	Het
Fxr1	A	G	3: 34,103,333 (GRCm39)	E221G	probably damaging	Het
Gpatch11	A	G	17: 79,151,272 (GRCm39)	T228A	probably damaging	Het
Greb1	G	T	12: 16,738,592 (GRCm39)	T1457K	probably damaging	Het
Ighm	T	A	12: 113,382,596 (GRCm39)		probably benign	Het
Ints12	G	A	3: 132,815,126 (GRCm39)	M444I	possibly damaging	Het
Lmx1b	G	A	2: 33,457,297 (GRCm39)	Q168*	probably null	Het
Ltbp3	C	A	19: 5,801,434 (GRCm39)	N659K	probably benign	Het
Micos13	A	G	17: 56,915,889 (GRCm39)	F55S	probably damaging	Het
Mrpl20	G	T	4: 155,888,329 (GRCm39)	V43F	possibly damaging	Het
Nlgn1	T	C	3: 25,487,860 (GRCm39)	N825S	possibly damaging	Het
Or5d36	T	A	2: 87,901,583 (GRCm39)	T48S	probably benign	Het
Or5p67	A	T	7: 107,922,757 (GRCm39)	V42E	possibly damaging	Het
Or8k3b	C	A	2: 86,520,896 (GRCm39)	C141F	possibly damaging	Het
Pccb	C	T	9: 100,912,250 (GRCm39)	R79Q	probably damaging	Het
Peg10	G	A	6: 4,755,029 (GRCm39)	R270H	possibly damaging	Het
Pttg1ip2	A	T	5: 5,507,283 (GRCm39)		probably null	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Timm29	T	C	9: 21,504,887 (GRCm39)	M185T	probably damaging	Het
Tmem92	C	T	11: 94,669,873 (GRCm39)	C86Y	probably benign	Het
Tnfrsf8	C	T	4: 145,011,895 (GRCm39)		probably null	Het
Tnks1bp1	T	A	2: 84,900,344 (GRCm39)	C1433*	probably null	Het
Utp14b	T	A	1: 78,642,442 (GRCm39)	D113E	possibly damaging	Het
Vmn2r110	T	A	17: 20,803,360 (GRCm39)	Y405F	probably damaging	Het
Wiz	A	G	17: 32,576,671 (GRCm39)	S628P	probably benign	Het
Xrcc4	T	C	13: 90,210,196 (GRCm39)	T83A	probably benign	Het

Other mutations in Slc4a4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00827:Slc4a4	APN	5	89,327,545 (GRCm39)	missense	probably benign	0.01
IGL00976:Slc4a4	APN	5	89,102,657 (GRCm39)	missense	probably damaging	1.00
IGL01074:Slc4a4	APN	5	89,327,633 (GRCm39)	missense	probably damaging	1.00
IGL01120:Slc4a4	APN	5	89,280,238 (GRCm39)	missense	probably damaging	1.00
IGL01284:Slc4a4	APN	5	89,277,532 (GRCm39)	missense	probably benign	0.22
IGL01375:Slc4a4	APN	5	89,327,593 (GRCm39)	missense	probably damaging	1.00
IGL01399:Slc4a4	APN	5	89,376,794 (GRCm39)	missense	probably damaging	1.00
IGL01487:Slc4a4	APN	5	89,376,715 (GRCm39)	missense	probably benign	0.19
IGL02501:Slc4a4	APN	5	89,277,508 (GRCm39)	missense	probably benign	0.13
IGL03104:Slc4a4	APN	5	89,297,231 (GRCm39)	missense	probably damaging	1.00
IGL03157:Slc4a4	APN	5	89,304,372 (GRCm39)	missense	probably damaging	0.99
IGL03205:Slc4a4	APN	5	89,297,189 (GRCm39)	missense	probably benign	0.00
IGL03356:Slc4a4	APN	5	89,270,342 (GRCm39)	missense	probably benign	0.00
IGL03372:Slc4a4	APN	5	89,304,285 (GRCm39)	missense	probably damaging	1.00
IGL03382:Slc4a4	APN	5	89,376,695 (GRCm39)	missense	probably damaging	1.00
camera	UTSW	5	89,280,366 (GRCm39)	missense	probably damaging	1.00
pixels	UTSW	5	89,270,262 (GRCm39)	missense	probably damaging	0.99
Shutter	UTSW	5	89,373,807 (GRCm39)	missense	probably damaging	1.00
Tetrapod	UTSW	5	89,376,831 (GRCm39)	missense	probably damaging	1.00
Therapod	UTSW	5	89,283,581 (GRCm39)	missense	probably damaging	1.00
tripod	UTSW	5	89,297,192 (GRCm39)	missense	possibly damaging	0.52
BB008:Slc4a4	UTSW	5	89,318,640 (GRCm39)	missense	probably benign	0.00
BB018:Slc4a4	UTSW	5	89,318,640 (GRCm39)	missense	probably benign	0.00
PIT4515001:Slc4a4	UTSW	5	89,281,112 (GRCm39)	missense	probably damaging	1.00
PIT4544001:Slc4a4	UTSW	5	89,186,402 (GRCm39)	missense	probably damaging	1.00
R0007:Slc4a4	UTSW	5	89,186,437 (GRCm39)	missense	probably damaging	1.00
R0052:Slc4a4	UTSW	5	89,304,195 (GRCm39)	missense	possibly damaging	0.71
R0052:Slc4a4	UTSW	5	89,304,195 (GRCm39)	missense	possibly damaging	0.71
R0054:Slc4a4	UTSW	5	89,304,195 (GRCm39)	missense	possibly damaging	0.71
R0055:Slc4a4	UTSW	5	89,304,195 (GRCm39)	missense	possibly damaging	0.71
R0230:Slc4a4	UTSW	5	89,304,195 (GRCm39)	missense	possibly damaging	0.71
R0234:Slc4a4	UTSW	5	89,304,195 (GRCm39)	missense	possibly damaging	0.71
R0234:Slc4a4	UTSW	5	89,304,195 (GRCm39)	missense	possibly damaging	0.71
R0632:Slc4a4	UTSW	5	89,277,500 (GRCm39)	missense	probably damaging	1.00
R1199:Slc4a4	UTSW	5	89,363,653 (GRCm39)	critical splice donor site	probably null
R1597:Slc4a4	UTSW	5	89,283,587 (GRCm39)	missense	probably benign	0.01
R1783:Slc4a4	UTSW	5	89,280,273 (GRCm39)	missense	probably damaging	1.00
R1813:Slc4a4	UTSW	5	89,194,167 (GRCm39)	missense	probably damaging	0.98
R1896:Slc4a4	UTSW	5	89,194,167 (GRCm39)	missense	probably damaging	0.98
R2000:Slc4a4	UTSW	5	89,176,206 (GRCm39)	missense	probably damaging	1.00
R2139:Slc4a4	UTSW	5	89,194,123 (GRCm39)	missense	probably damaging	1.00
R2163:Slc4a4	UTSW	5	89,362,435 (GRCm39)	missense	probably damaging	1.00
R2513:Slc4a4	UTSW	5	89,304,257 (GRCm39)	missense	probably benign	0.00
R2873:Slc4a4	UTSW	5	89,283,623 (GRCm39)	missense	probably damaging	1.00
R2995:Slc4a4	UTSW	5	89,082,673 (GRCm39)	missense	probably damaging	1.00
R3054:Slc4a4	UTSW	5	89,373,807 (GRCm39)	missense	probably damaging	1.00
R3055:Slc4a4	UTSW	5	89,373,807 (GRCm39)	missense	probably damaging	1.00
R3055:Slc4a4	UTSW	5	89,280,366 (GRCm39)	missense	probably damaging	1.00
R3617:Slc4a4	UTSW	5	89,382,663 (GRCm39)	missense	probably benign	0.00
R3856:Slc4a4	UTSW	5	89,380,698 (GRCm39)	missense	probably benign	0.00
R3863:Slc4a4	UTSW	5	89,283,507 (GRCm39)	missense	possibly damaging	0.95
R3896:Slc4a4	UTSW	5	89,345,625 (GRCm39)	splice site	probably benign
R4007:Slc4a4	UTSW	5	89,362,452 (GRCm39)	missense	probably damaging	1.00
R4616:Slc4a4	UTSW	5	89,186,420 (GRCm39)	missense	probably damaging	1.00
R4740:Slc4a4	UTSW	5	89,373,753 (GRCm39)	missense	probably damaging	1.00
R5009:Slc4a4	UTSW	5	89,297,157 (GRCm39)	critical splice acceptor site	probably null
R5119:Slc4a4	UTSW	5	89,102,721 (GRCm39)	missense	probably null	0.97
R5228:Slc4a4	UTSW	5	89,304,384 (GRCm39)	missense	possibly damaging	0.50
R5394:Slc4a4	UTSW	5	89,345,623 (GRCm39)	critical splice donor site	probably null
R5396:Slc4a4	UTSW	5	89,194,076 (GRCm39)	missense	probably benign	0.00
R5662:Slc4a4	UTSW	5	89,176,103 (GRCm39)	missense	probably damaging	0.96
R5664:Slc4a4	UTSW	5	89,176,103 (GRCm39)	missense	probably damaging	0.96
R6021:Slc4a4	UTSW	5	89,188,261 (GRCm39)	intron	probably benign
R6088:Slc4a4	UTSW	5	89,345,563 (GRCm39)	missense	probably benign	0.12
R6337:Slc4a4	UTSW	5	89,194,231 (GRCm39)	missense	probably benign	0.21
R6416:Slc4a4	UTSW	5	89,327,588 (GRCm39)	missense	probably benign	0.26
R6452:Slc4a4	UTSW	5	89,376,839 (GRCm39)	missense	probably benign	0.05
R6524:Slc4a4	UTSW	5	89,380,623 (GRCm39)	missense	probably benign	0.01
R6566:Slc4a4	UTSW	5	89,297,192 (GRCm39)	missense	possibly damaging	0.52
R6727:Slc4a4	UTSW	5	89,318,624 (GRCm39)	missense	probably benign	0.00
R6844:Slc4a4	UTSW	5	89,376,831 (GRCm39)	missense	probably damaging	1.00
R6970:Slc4a4	UTSW	5	89,327,690 (GRCm39)	missense	probably damaging	0.98
R7021:Slc4a4	UTSW	5	89,188,205 (GRCm39)	splice site	probably null
R7180:Slc4a4	UTSW	5	89,194,095 (GRCm39)	missense	probably damaging	0.97
R7197:Slc4a4	UTSW	5	89,082,433 (GRCm39)	intron	probably benign
R7246:Slc4a4	UTSW	5	89,270,262 (GRCm39)	missense	probably damaging	0.99
R7309:Slc4a4	UTSW	5	89,318,610 (GRCm39)	missense	probably benign
R7412:Slc4a4	UTSW	5	89,362,506 (GRCm39)	splice site	probably null
R7492:Slc4a4	UTSW	5	89,277,509 (GRCm39)	missense	possibly damaging	0.92
R7561:Slc4a4	UTSW	5	89,347,556 (GRCm39)	missense	probably damaging	1.00
R7577:Slc4a4	UTSW	5	89,373,726 (GRCm39)	missense	probably damaging	0.97
R7609:Slc4a4	UTSW	5	89,283,545 (GRCm39)	missense	probably damaging	1.00
R7781:Slc4a4	UTSW	5	89,376,791 (GRCm39)	missense	possibly damaging	0.78
R7931:Slc4a4	UTSW	5	89,318,640 (GRCm39)	missense	probably benign	0.00
R7950:Slc4a4	UTSW	5	89,206,137 (GRCm39)	splice site	probably null
R8078:Slc4a4	UTSW	5	89,327,566 (GRCm39)	missense	probably benign	0.00
R8313:Slc4a4	UTSW	5	89,194,122 (GRCm39)	missense	possibly damaging	0.84
R8332:Slc4a4	UTSW	5	89,327,680 (GRCm39)	missense	probably benign	0.11
R8534:Slc4a4	UTSW	5	89,283,581 (GRCm39)	missense	probably damaging	1.00
R8735:Slc4a4	UTSW	5	89,280,301 (GRCm39)	missense	probably damaging	1.00
R8786:Slc4a4	UTSW	5	89,232,549 (GRCm39)	missense	probably benign	0.07
R8968:Slc4a4	UTSW	5	89,232,512 (GRCm39)	missense	probably benign
R9014:Slc4a4	UTSW	5	89,280,245 (GRCm39)	missense	probably damaging	1.00
R9031:Slc4a4	UTSW	5	89,205,568 (GRCm39)	intron	probably benign
R9195:Slc4a4	UTSW	5	89,281,055 (GRCm39)	missense	possibly damaging	0.82
R9236:Slc4a4	UTSW	5	89,194,158 (GRCm39)	nonsense	probably null
R9261:Slc4a4	UTSW	5	89,347,568 (GRCm39)	missense	probably damaging	1.00
R9325:Slc4a4	UTSW	5	89,376,756 (GRCm39)	missense	probably damaging	1.00
R9401:Slc4a4	UTSW	5	89,327,525 (GRCm39)	missense	probably damaging	1.00
R9457:Slc4a4	UTSW	5	89,362,432 (GRCm39)	missense	probably damaging	1.00
R9462:Slc4a4	UTSW	5	89,194,131 (GRCm39)	missense	probably damaging	1.00
R9681:Slc4a4	UTSW	5	89,102,723 (GRCm39)	nonsense	probably null
R9709:Slc4a4	UTSW	5	89,188,205 (GRCm39)	splice site	probably null
Z1177:Slc4a4	UTSW	5	89,280,318 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AATCACTCCTGGCTGGCTAAG -3'
(R):5'- AGGAACCTGTGCCAGTTATTG -3'

Sequencing Primer
(F):5'- AGATAACACATCGACTTTTTCTCC -3'
(R):5'- GGAACCTGTGCCAGTTATTGAACTC -3'

Posted On

2015-02-05