IGDRPT (Indian Genetic Disease Risk Prediction Tool)

Disease Name: Autosomal recessive infantile malignant osteopetrosis

1 .Inheritance

Autosomal Recessive

2. Gene Name

TCIRG1

3. Protein Name

V-type proton ATPase 116 kDa subunit a 3

4. Chromosomal Location

11q13.4-q13.5

5. Protein Sequence

>sp|Q13488|VPP3_HUMAN V-type proton ATPase 116 kDa subunit a3 OS=Homo sapiens OX=9606 GN=TCIRG1 PE=1 SV=3

MGSMFRSEEVALVQLFLPTAAAYTCVSRLGELGLVEFRDLNASVSAFQRRFVVDVRRCEE

LEKTFTFLQEEVRRAGLVLPPPKGRLPAPPPRDLLRIQEETERLAQELRDVRGNQQALRA

QLHQLQLHAAVLRQGHEPQLAAAHTDGASERTPLLQAPGGPHQDLRVNFVAGAVEPHKAP

ALERLLWRACRGFLIASFRELEQPLEHPVTGEPATWMTFLISYWGEQIGQKIRKITDCFH

CHVFPFLQQEEARLGALQQLQQQSQELQEVLGETERFLSQVLGRVLQLLPPGQVQVHKMK

AVYLALNQCSVSTTHKCLIAEAWCSVRDLPALQEALRDSSMEEGVSAVAHRIPCRDMPPT

LIRTNRFTASFQGIVDAYGVGRYQEVNPAPYTIITFPFLFAVMFGDVGHGLLMFLFALAM

VLAENRPAVKAAQNEIWQTFFRGRYLLLLMGLFSIYTGFIYNECFSRATSIFPSGWSVAA

MANQSGWSDAFLAQHTMLTLDPNVTGVFLGPYPFGIDPIWSLAANHLSFLNSFKMKMSVI

LGVVHMAFGVVLGVFNHVHFGQRHRLLLETLPELTFLLGLFGYLVFLVIYKWLCVWAARA

ASAPSILIHFINMFLFSHSPSNRLLYPRQEVVQATLVVLALAMVPILLLGTPLHLLHRHR

RRLRRRPADRQEENKAGLLDLPDASVNGWSSDEEKAGGLDDEEEAELVPSEVLMHQAIHT

IEFCLGCVSNTASYLRLWALSLAHAQLSEVLWAMVMRIGLGLGREVGVAAVVLVPIFAAF

AVMTVAILLVMEGLSAFLHALRLHWVEFQNKFYSGTGYKLSPFTFAATDD

6. Gene Sequence

>NM_006019.2 Homo sapiens T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3 (TCIRG1), transcript variant 1, mRNA

GCGGCGCCTAGTCCCGGGCTGGCGGGAGTGCAGTTCTGAGTCCCGCCCGGCGTGCGCGGAGCGGGGCAGC

CAGCAGCGGAGGCGCGGCGCGCAGCACACCCGGGGACCATGGGCTCCATGTTCCGGAGCGAGGAGGTGGC

CCTGGTCCAGCTCTTTCTGCCCACAGCGGCTGCCTACACCTGCGTGAGTCGGCTGGGCGAGCTGGGCCTC

GTGGAGTTCAGAGACCTCAACGCCTCGGTGAGCGCCTTCCAGAGACGCTTTGTGGTTGATGTTCGGCGCT

GTGAGGAGCTGGAGAAGACCTTCACCTTCCTGCAGGAGGAGGTGCGGCGGGCTGGGCTGGTCCTGCCCCC

GCCAAAGGGGAGGCTGCCGGCACCCCCACCCCGGGACCTGCTGCGCATCCAGGAGGAGACGGAGCGCCTG

GCCCAGGAGCTGCGGGATGTGCGGGGCAACCAGCAGGCCCTGCGGGCCCAGCTGCACCAGCTGCAGCTCC

ACGCCGCCGTGCTACGCCAGGGCCATGAACCTCAGCTGGCAGCCGCCCACACAGATGGGGCCTCAGAGAG

GACGCCCCTGCTCCAGGCCCCCGGGGGGCCGCACCAGGACCTGAGGGTCAACTTTGTGGCAGGTGCCGTG

GAGCCCCACAAGGCCCCTGCCCTAGAGCGCCTGCTCTGGAGGGCCTGCCGCGGCTTCCTCATTGCCAGCT

TCAGGGAGCTGGAGCAGCCGCTGGAGCACCCCGTGACGGGCGAGCCAGCCACGTGGATGACCTTCCTCAT

CTCCTACTGGGGTGAGCAGATCGGACAGAAGATCCGCAAGATCACGGACTGCTTCCACTGCCACGTCTTC

CCGTTTCTGCAGCAGGAGGAGGCCCGCCTCGGGGCCCTGCAGCAGCTGCAACAGCAGAGCCAGGAGCTGC

AGGAGGTCCTCGGGGAGACAGAGCGGTTCCTGAGCCAGGTGCTAGGCCGGGTGCTGCAGCTGCTGCCGCC

AGGGCAGGTGCAGGTCCACAAGATGAAGGCCGTGTACCTGGCCCTGAACCAGTGCAGCGTGAGCACCACG

CACAAGTGCCTCATTGCCGAGGCCTGGTGCTCTGTGCGAGACCTGCCCGCCCTGCAGGAGGCCCTGCGGG

ACAGCTCGATGGAGGAGGGAGTGAGTGCCGTGGCTCACCGCATCCCCTGCCGGGACATGCCCCCCACACT

CATCCGCACCAACCGCTTCACGGCCAGCTTCCAGGGCATCGTGGATGCCTACGGCGTGGGCCGCTACCAG

GAGGTCAACCCCGCTCCCTACACCATCATCACCTTCCCCTTCCTGTTTGCTGTGATGTTCGGGGATGTGG

GCCACGGGCTGCTCATGTTCCTCTTCGCCCTGGCCATGGTCCTTGCGGAGAACCGACCGGCTGTGAAGGC

CGCGCAGAACGAGATCTGGCAGACTTTCTTCAGGGGCCGCTACCTGCTCCTGCTTATGGGCCTGTTCTCC

ATCTACACCGGCTTCATCTACAACGAGTGCTTCAGTCGCGCCACCAGCATCTTCCCCTCGGGCTGGAGTG

TGGCCGCCATGGCCAACCAGTCTGGCTGGAGTGATGCATTCCTGGCCCAGCACACGATGCTTACCCTGGA

TCCCAACGTCACCGGTGTCTTCCTGGGACCCTACCCCTTTGGCATCGATCCTATTTGGAGCCTGGCTGCC

AACCACTTGAGCTTCCTCAACTCCTTCAAGATGAAGATGTCCGTCATCCTGGGCGTCGTGCACATGGCCT

TTGGGGTGGTCCTCGGAGTCTTCAACCACGTGCACTTTGGCCAGAGGCACCGGCTGCTGCTGGAGACGCT

GCCGGAGCTCACCTTCCTGCTGGGACTCTTCGGTTACCTCGTGTTCCTAGTCATCTACAAGTGGCTGTGT

GTCTGGGCTGCCAGGGCCGCCTCGGCCCCCAGCATCCTCATCCACTTCATCAACATGTTCCTCTTCTCCC

ACAGCCCCAGCAACAGGCTGCTCTACCCCCGGCAGGAGGTGGTCCAGGCCACGCTGGTGGTCCTGGCCTT

GGCCATGGTGCCCATCCTGCTGCTTGGCACACCCCTGCACCTGCTGCACCGCCACCGCCGCCGCCTGCGG

AGGAGGCCCGCTGACCGACAGGAGGAAAACAAGGCCGGGTTGCTGGACCTGCCTGACGCATCTGTGAATG

GCTGGAGCTCCGATGAGGAAAAGGCAGGGGGCCTGGATGATGAAGAGGAGGCCGAGCTCGTCCCCTCCGA

GGTGCTCATGCACCAGGCCATCCACACCATCGAGTTCTGCCTGGGCTGCGTCTCCAACACCGCCTCCTAC

CTGCGCCTGTGGGCCCTGAGCCTGGCCCACGCCCAGCTGTCCGAGGTTCTGTGGGCCATGGTGATGCGCA

TAGGCCTGGGCCTGGGCCGGGAGGTGGGCGTGGCGGCTGTGGTGCTGGTCCCCATCTTTGCCGCCTTTGC

CGTGATGACCGTGGCTATCCTGCTGGTGATGGAGGGACTCTCAGCCTTCCTGCACGCCCTGCGGCTGCAC

TGGGTGGAATTCCAGAACAAGTTCTACTCAGGCACGGGCTACAAGCTGAGTCCCTTCACCTTCGCTGCCA

CAGATGACTAGGGCCCACTGCAGGTCCTGCCAGACCTCCTTCCTGACCTCTGAGGCAGGAGAGGAATAAA

GACGGTCCGCCCTGGCAGTGAAAAAAAAAAAAAAAAAAAA

7. Motif

Pfam (4 motifs)

Pfam	Position(Independent E-value)	Description
V_ATPase_I	28..825(8e-280)	PF01496, V-type ATPase 116kDa subunit family
Romo1	534..576(0.047)	PF10247, Reactive mitochondrial oxygen species modulator 1
APG6_N	94..137(0.4)	PF17675, Apg6 coiled-coil region
DUF2730	98..131(0.43)	PF10805, Protein of unknown function (DUF2730)

8. Evolutionary Relationship

Evolutionary analysis by Maximum Likelihood method

The evolutionary history was inferred by using the Maximum Likelihood method and JTT matrix-based model [1]. The tree with the highest log likelihood (-17369.52) is shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The proportion of sites where at least 1 unambiguous base is present in at least 1 sequence for each descendent clade is shown next to each internal node in the tree. This analysis involved 100 amino acid sequences. There were a total of 1451 positions in the final dataset.

9. SNP

SNP	COORDINATE	AMINO ACID CHANGE	GENE ID	TRANSCRIPT ID	PROTEIN ID	SIFT SCORE	SIFT MEDIAN	SIFT PREDICTION
rs137853150	67814947	G405R	ENSG00000110719	ENST00000265686	ENSP00000265686	0	2.67	DELETERIOUS
rs137853150	67814947	R208Q	ENSG00000110719	ENST00000529364	ENSP00000431437
rs137853150	67814947	G189R	ENSG00000110719	ENST00000532635	ENSP00000434407	0	2.65	DELETERIOUS
rs137853151	67815139	R444L	ENSG00000110719	ENST00000265686	ENSP00000265686	0	2.67	DELETERIOUS
rs137853151	67815139	R228L	ENSG00000110719	ENST00000532635	ENSP00000434407	0	2.65	DELETERIOUS
rs137853151	67815139	P247P	ENSG00000110719	ENST00000529364	ENSP00000431437	0.342	4.32	TOLERATED

Evolutionary analysis of coding SNPs

SNP	Substitution	Probability of deleterious effect	Pdel
rs137853150	G405R	probably damaging	0.95
rs137853151	R444L	probably damaging	0.89

Provean

SNP Id’s	Amino Acid Change	Probability	Prediction	Score
rs137853150	G405R	Deleterious	Damaging	-7.5
rs137853150	G189R	Deleterious	Damaging	-7.65
rs137853151	R444L	Deleterious	Damaging	-6.71
rs137853151	R228L	Deleterious	Damaging	-6.77

SNAP 2

Wildetype Amino Acid	Position	Variant Amino Acid	Predicted Effect	Score	Expected Accurancy
G	405	R	Effect	77	90%
G	189	R	Neutral	65	87%
R	444	L	Effect	35	57%
R	228	L	Neutral	87	75%

Polyphen 2

Rs_Id	Mutation Probability	Score
rs137853150	Probably damaging	0.999
rs137853150	Possibly damaging	0.999
rs137853151	Probably damaging	1.00
rs137853151	Probably damaging	0.98

Hope Prediction

Rs_Ids	Mutation	Mapping Issues	AA Variant	Function Impact	Score
rs137853150	TCIRG1_G405R		G405R	High	6.62
rs137853150	TCIRG1_G189R		G189R	Medium	2.16
rs137853151	TCIRG1_R444L	Uniprot Residue:G	R444L	Medium	4.3
rs137853151	TCIRG1_R228L		R228L	Low	0.82

10. Active Site

Rank	C-Score	Cluster Size	PDB Hit	Lig Name	Consensus Building Residues
1	0.04	3	2o011	CLA	806,807
2	0.04	3	2yfcB	MN	265,266,269
3	0.03	2	3elmA	CA	454,457
4	0.03	2	3a0hK	CLA	396,400
5	0.03	2	3tv5C	RCP	796,797,800
6	0.01	1	5d0fA	MTT	406,527,530,531,534
7	0.01	1	2eulA	ZN	269,273
8	0.01	1	5cteB	57L	545,546,549,550
9	0.01	1	5cx6A	MG	567,572
10	0.01	1	1izlB	CLA	118,270

11. Primary Sequence Analysis

Number of amino acids

830

Molecular weight

92968.03

Theoretical pI

6.66

Amino acid composition

Ala (A) 83 10.0%

Arg (R) 55 6.6%

Asn (N) 20 2.4%

Asp (D) 23 2.8%

Cys (C) 13 1.6%

Gln (Q) 45 5.4%

Glu (E) 53 6.4%

Gly (G) 53 6.4%

His (H) 29 3.5%

Ile (I) 29 3.5%

Leu (L) 118 14.2%

Lys (K) 16 1.9%

Met (M) 22 2.7%

Phe (F) 51 6.1%

Pro (P) 44 5.3%

Ser (S) 44 5.3%

Thr (T) 35 4.2%

Trp (W) 14 1.7%

Tyr (Y) 16 1.9%

Val (V) 67 8.1%

Pyl (O) 0 0.0%

Sec (U) 0 0.0%

Total number of negatively charged residues (Asp + Glu)

Total number of positively charged residues (Arg + Lys)

Formula

C₄₂₃₂H₆₅₉₆N₁₁₄₈O₁₁₄₃S₃₅

Total number of atoms(12269)

13154

Instability index(II)

49.89

Stability

Unstable

Aliphatic index(AI)

102.48

GRAVY

0.176

12. Secondary structure analysis

Alpha helix (Hh) : 435 is 52.41%

310 helix (Gg) : 0 is 0.00%

Pi helix (Ii) : 0 is 0.00%

Beta bridge (Bb) : 0 is 0.00%

Extended strand (Ee) : 101 is 12.17%

Beta turn (Tt) : 26 is 3.13%

Bend region (Ss) : 0 is 0.00%

Random coil (Cc) : 268 is 32.29%

Ambiguous states (?) : 0 is 0.00%

Other states : 0 is 0.00%

Secondary Structure Prediction

Amino Acid Type

13. Enzymes

Name of enzyme	No. of cleavages
Arg-C proteinase	55
Asp-N endopeptidase	23
Asp-N endopeptidase + N-terminal Glu	76
BNPS-Skatole	14
CNBr	22
Chymotrypsin-high specificity (C-term to [FYW], not before P)	75
Chymotrypsin-low specificity (C-term to [FYWML], not before P)	233
Clostripain	55
Formic acid	23
Glutamyl endopeptidase	53
Iodosobenzoic acid	14
Hydroxylamine	1
Iodosobenzoic acid	14
LysC	16
LysN	16
NTCB (2-nitro-5-thiocyanobenzoic acid)	13
Pepsin (pH1.3)	221
Pepsin (pH>2)	260
Proline-endopeptidase	3
Proteinase K	466
Staphylococcal peptidase I	43
Thermolysin	317
Trypsin	67

14. Epitope

Rank	Start position	Sequence	Score	Prediction
1	75	AGLVLPPPKGRLPAPP	0.91	Epitope
1	714	MHQAIHTIEFCLGCVS	0.91	Epitope
2	138	PQLAAAHTDGASERTP	0.90	Epitope
3	83	KGRLPAPPPRDLLRIQ	0.88	Epitope
3	160	GPHQDLRVNFVAGAVE	0.88	Epitope
4	814	SGTGYKLSPFTFAATD	0.87	Epitope
4	694	EKAGGLDDEEEAELVP	0.87	Epitope
4	378	YGVGRYQEVNPAPYTI	0.87	Epitope
5	503	NVTGVFLGPYPFGIDP	0.86	Epitope
5	479	AAMANQSGWSDAFLAQ	0.86	Epitope

15. Protein-Protein Interaction

No of Nodes	11
No of Edges	55
Avg node degree	10
avg. local clustering coefficient	1
expected number of e, dges	10
p-value	< 1.0e-16
Protein – Protein Interaction network

16. MRNA

RNA Base Pairing Probability Plot