Mutagenetix > Incidental Mutation

Incidental Mutation 'R9200:Sectm1a'

698188

Institutional Source

Beutler Lab

Gene Symbol

Sectm1a

Ensembl Gene

ENSMUSG00000025165

Gene Name

secreted and transmembrane 1A

Synonyms

MMRRC Submission

068957-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.051) question?

Stock #

R9200 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

120958233-120972046 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 120960473 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 114 (Y114C)

Ref Sequence

ENSEMBL: ENSMUSP00000026162 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026162] [ENSMUST00000100126] [ENSMUST00000106119] [ENSMUST00000106120]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000026162
AA Change: Y114C

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

SMART Domains

Protein: ENSMUSP00000026162
Gene: ENSMUSG00000025165
AA Change: Y114C

Domain	Start	End	E-Value	Type
signal peptide	1	27	N/A	INTRINSIC
Blast:IG	39	133	2e-64	BLAST
SCOP:d1biha2	42	114	3e-3	SMART
transmembrane domain	165	187	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000100126

SMART Domains

Protein: ENSMUSP00000097702
Gene: ENSMUSG00000025165

Domain	Start	End	E-Value	Type
signal peptide	1	27	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000106119

SMART Domains

Protein: ENSMUSP00000101725
Gene: ENSMUSG00000025165

Domain	Start	End	E-Value	Type
signal peptide	1	27	N/A	INTRINSIC
transmembrane domain	62	84	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000106120
AA Change: Y114C

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

SMART Domains

Protein: ENSMUSP00000101726
Gene: ENSMUSG00000025165
AA Change: Y114C

Domain	Start	End	E-Value	Type
signal peptide	1	27	N/A	INTRINSIC
Blast:IG	39	133	2e-64	BLAST
SCOP:d1biha2	42	114	2e-3	SMART
transmembrane domain	147	169	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

99% (71/72)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a transmembrane and secreted protein with characteristics of a type 1a transmembrane protein. It is found in a perinuclear Golgi-like pattern and thought to be involved in hematopoietic and/or immune system processes. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsm2	C	A	7: 119,179,839 (GRCm39)	Y352*	probably null	Het
Adh7	C	T	3: 137,927,567 (GRCm39)	R38C	probably benign	Het
Ankrd2	A	T	19: 42,028,871 (GRCm39)	T145S		Het
Anpep	T	C	7: 79,490,870 (GRCm39)	N241D	probably benign	Het
Apaf1	G	A	10: 90,845,102 (GRCm39)	L990F	probably benign	Het
Arsi	A	G	18: 61,049,836 (GRCm39)	T240A	possibly damaging	Het
Ascc3	A	G	10: 50,521,787 (GRCm39)	E434G	possibly damaging	Het
Atp2c2	A	T	8: 120,474,999 (GRCm39)	K535*	probably null	Het
B3galt4	A	G	17: 34,170,384 (GRCm39)		probably benign	Het
Brwd1	C	G	16: 95,839,154 (GRCm39)	C839S	probably benign	Het
Cars1	C	T	7: 143,129,654 (GRCm39)		probably null	Het
Catsperd	T	A	17: 56,935,229 (GRCm39)	V14D	unknown	Het
Ccdc150	A	C	1: 54,299,197 (GRCm39)	T58P	probably damaging	Het
Cdhr17	T	C	5: 17,006,659 (GRCm39)		probably null	Het
Cdon	A	G	9: 35,414,617 (GRCm39)	D1164G	probably benign	Het
Celsr1	G	T	15: 85,917,286 (GRCm39)	S229*	probably null	Het
Cic	A	C	7: 24,971,940 (GRCm39)	D557A	probably damaging	Het
Clip4	G	A	17: 72,117,884 (GRCm39)	G310R	probably damaging	Het
Dach1	G	T	14: 98,065,743 (GRCm39)	R695S	probably damaging	Het
Ddc	T	C	11: 11,765,388 (GRCm39)	N428S	possibly damaging	Het
Dnah6	G	A	6: 73,004,497 (GRCm39)	T3822I	probably benign	Het
Dnmt1	T	A	9: 20,819,896 (GRCm39)	M1535L	probably benign	Het
Edc4	T	C	8: 106,617,051 (GRCm39)		probably null	Het
Emilin2	A	G	17: 71,581,229 (GRCm39)	I499T	possibly damaging	Het
Etl4	A	G	2: 20,786,702 (GRCm39)	D766G	probably damaging	Het
Fes	T	C	7: 80,032,140 (GRCm39)	Q414R	probably benign	Het
Fhod1	A	G	8: 106,058,072 (GRCm39)	V844A	probably benign	Het
Fshr	A	T	17: 89,354,103 (GRCm39)	V85E	probably benign	Het
Gc	T	C	5: 89,593,236 (GRCm39)	N61S	probably benign	Het
Hapstr1	T	C	16: 8,673,898 (GRCm39)	L275P	possibly damaging	Het
Il18rap	C	T	1: 40,582,177 (GRCm39)	T366M	probably benign	Het
Itga1	A	T	13: 115,104,997 (GRCm39)	I1059N	possibly damaging	Het
Itpr3	T	A	17: 27,326,636 (GRCm39)	V1426E	probably damaging	Het
Jag1	T	A	2: 136,929,044 (GRCm39)	Y804F	probably benign	Het
Lama3	A	G	18: 12,605,297 (GRCm39)	T1084A	probably benign	Het
Mdn1	A	G	4: 32,760,791 (GRCm39)	D4952G	probably benign	Het
Mmrn1	A	G	6: 60,953,860 (GRCm39)	T714A	probably damaging	Het
Nab1	T	A	1: 52,529,525 (GRCm39)	H124L	possibly damaging	Het
Nacc2	A	G	2: 25,980,118 (GRCm39)	F106S	probably damaging	Het
Nbeal1	T	C	1: 60,320,425 (GRCm39)	I2006T	probably damaging	Het
Nkpd1	C	A	7: 19,257,683 (GRCm39)	H487Q	probably benign	Het
Nop2	G	A	6: 125,117,843 (GRCm39)		probably null	Het
Or10ag54	T	A	2: 87,100,055 (GRCm39)	M310K	probably benign	Het
Or5b124	A	G	19: 13,610,595 (GRCm39)	N40S	probably damaging	Het
Otud6b	A	T	4: 14,811,712 (GRCm39)	Y310*	probably null	Het
Phyh	A	T	2: 4,932,247 (GRCm39)	Y111F	probably benign	Het
Pon3	A	G	6: 5,240,863 (GRCm39)	L106P	probably benign	Het
Ppp6r3	T	C	19: 3,519,748 (GRCm39)	D615G	probably damaging	Het
Pramel23	G	A	4: 143,423,856 (GRCm39)	P311L	possibly damaging	Het
Prdm10	G	A	9: 31,268,438 (GRCm39)	V796I	probably damaging	Het
Prkdc	G	T	16: 15,523,153 (GRCm39)	V1192F	probably damaging	Het
R3hdm2	T	G	10: 127,293,521 (GRCm39)	S142A	probably damaging	Het
Rab39	T	C	9: 53,597,665 (GRCm39)	N200S	probably benign	Het
Rcc2	A	G	4: 140,445,664 (GRCm39)	I441V	probably benign	Het
Rxra	G	A	2: 27,627,496 (GRCm39)	V72I	possibly damaging	Het
Ryr1	T	G	7: 28,794,524 (GRCm39)	Q1252P	probably benign	Het
Smim1	T	C	4: 154,108,276 (GRCm39)		probably null	Het
Smpd2	C	T	10: 41,363,561 (GRCm39)	D301N	probably benign	Het
Smyd3	T	C	1: 179,232,963 (GRCm39)	D139G	probably benign	Het
Sox13	C	T	1: 133,313,743 (GRCm39)	C399Y	probably damaging	Het
Tars3	A	G	7: 65,302,013 (GRCm39)	E179G	probably benign	Het
Tas2r138	A	G	6: 40,589,494 (GRCm39)	F251L	probably damaging	Het
Tesk1	A	G	4: 43,447,307 (GRCm39)	E565G	probably damaging	Het
Tm2d1	A	T	4: 98,246,200 (GRCm39)	F201I	possibly damaging	Het
Tom1l2	C	A	11: 60,120,942 (GRCm39)	D501Y	probably benign	Het
Trim39	G	T	17: 36,579,667 (GRCm39)	T96K	probably benign	Het
Ubash3a	A	G	17: 31,436,971 (GRCm39)	H196R	probably damaging	Het
Unc13b	A	G	4: 43,257,352 (GRCm39)	E1206G	possibly damaging	Het
Usp17lc	A	T	7: 103,068,105 (GRCm39)	T467S	probably benign	Het
Vmn1r128	T	C	7: 21,083,316 (GRCm39)	S7P	possibly damaging	Het
Vmn1r185	T	A	7: 26,311,073 (GRCm39)	H144L	possibly damaging	Het
Wfdc6b	A	T	2: 164,455,708 (GRCm39)	R12S	possibly damaging	Het
Zmynd8	A	T	2: 165,682,005 (GRCm39)	D175E	probably benign	Het

Other mutations in Sectm1a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01664:Sectm1a	APN	11	120,959,870 (GRCm39)	missense	possibly damaging	0.55
R0571:Sectm1a	UTSW	11	120,959,928 (GRCm39)	intron	probably benign
R1987:Sectm1a	UTSW	11	120,960,506 (GRCm39)	missense	probably damaging	1.00
R2023:Sectm1a	UTSW	11	120,960,408 (GRCm39)	splice site	probably benign
R3157:Sectm1a	UTSW	11	120,959,603 (GRCm39)	missense	probably benign	0.19
R3158:Sectm1a	UTSW	11	120,959,603 (GRCm39)	missense	probably benign	0.19
R4463:Sectm1a	UTSW	11	120,960,477 (GRCm39)	missense	probably benign
R4664:Sectm1a	UTSW	11	120,960,552 (GRCm39)	missense	possibly damaging	0.76
R7241:Sectm1a	UTSW	11	120,960,708 (GRCm39)	missense	possibly damaging	0.46
R7418:Sectm1a	UTSW	11	120,960,119 (GRCm39)	splice site	probably null
R7712:Sectm1a	UTSW	11	120,959,631 (GRCm39)	missense	probably damaging	0.99
R8990:Sectm1a	UTSW	11	120,960,701 (GRCm39)	missense	probably damaging	1.00
R9100:Sectm1a	UTSW	11	120,960,569 (GRCm39)	missense	possibly damaging	0.90
R9718:Sectm1a	UTSW	11	120,960,490 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- CAGTGGAGACTCTTTCCACACC -3'
(R):5'- ATCTCTAACACCTTCACCGATG -3'

Sequencing Primer
(F):5'- CGCAGGACAGATTAAGTTCCTCTG -3'
(R):5'- CGATGTCACCATCCAGCTG -3'

Posted On

2022-02-07