IGDRPT (Indian Genetic Disease Risk Prediction Tool)

Disease Name: Hypofibrinogenemia

1 .Inheritance

Autosomal Recessive

2. Gene Name

FGB

3. Protein Name

Fibrinogen beta chain

4. Chromosomal Location

4q28

5. Protein Sequence

>sp|P02675|FIBB_HUMAN Fibrinogen beta chain OS=Homo sapiens OX=9606 GN=FGB PE=1 SV=2

MKRMVSWSFHKLKTMKHLLLLLLCVFLVKSQGVNDNEEGFFSARGHRPLDKKREEAPSLR

PAPPPISGGGYRARPAKAAATQKKVERKAPDAGGCLHADPDLGVLCPTGCQLQEALLQQE

RPIRNSVDELNNNVEAVSQTSSSSFQYMYLLKDLWQKRQKQVKDNENVVNEYSSELEKHQ

LYIDETVNSNIPTNLRVLRSILENLRSKIQKLESDVSAQMEYCRTPCTVSCNIPVVSGKE

CEEIIRKGGETSEMYLIQPDSSVKPYRVYCDMNTENGGWTVIQNRQDGSVDFGRKWDPYK

QGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRMGPTELLIEMEDWKGDKVKAHYGGFT

VQNEANKYQISVNKYRGTAGNALMDGASQLMGENRTMTIHNGMFFSTYDRDNDGWLTSDP

RKQCSKEDGGGWWYNRCHAANPNGRYYWGGQYTWDMAKHGTDDGVVWMNWKGSWYSMRKM

SMKIRPFFPQQ

6. Gene Sequence

>NC_000004.12:154562980-154572807 Homo sapiens chromosome 4, GRCh38.p14 Primary Assembly

AGATATATATAGGATTGAAGATCTCTCAGTTAAGTCTACATGAAAAGGATGGTTTCTTGGAGCTTCCACA

AACTTAAAACCATGAAACATCTATTATTGCTACTATTGTGTGTTTTTCTAGTTAAGTCCCAAGGTGTCAA

CGACAATGAGGAGGTGAATTTTTTAAAGCATTATTATATTATTAGTAGTATTATTAATATAAGATGTAAC

ATAATCATATTATGTGCTTATTTTAATGAAATTAGCATTGCTTATAGTTATGAAATGGAATTGTTAACCT

CTGACTTATTGTATTTAAAGAATGTTTCATAGTATTTCTTATATAAAAACAAAGTAATTTCTTGTTTTCT

AGTTTATCACCTTTGTTTTCTTAAGATGAGGATGGCTTAGCTAATGTAAGATGTGTTTTTCTCACTTGCT

ATTCTGAGTACTGTGATTTTCATTTACTTCTAGCAATACAGGATTACAATTAAGAGGACAAGATCTGAAA

ATCTCACAAACTATAAAATAATAAAAGAGCAGAATTTTAAGATAAAAGAAACTGGTGGTAGGTAGATTGT

TCTTTGGTGAAGGAAGGTAATATATATTGTTACTGAGATTACTATTTATAAAAATTATAACTAAGCCTAA

AAGCAAAATACATCAAGTGTAATGATAGAAAATGAAATATTGCTTTTTTCAGATGAAAAGTTCAAATTAG

AGTTAGTGTGTATTGTTATTATTAATAGTTATGAAACACGGTTCAGTCTAATTTATTTATTTGTAGAACA

GTTTGTCCTCAACTATTATTTTTGCTGACTTATTGCTGTTAATTTGCAGTTACTAAAAATACAGAAATGC

ATTTAGGACAATGGATATTTAAGAAATTTAAATTTTATCATCAAACGTATCATGGCCAAATTTCTTACAT

ATAGCATAGTATCATTAAACTAGAAATAAGAATACACAATAATATTTAAATGAAGTGATTCATTTCGGAT

CATTATTGAGTTTCAAGGGAACTTGAGTGTTGTACTTATCAGACTCTACATGTAAGAACATATAGTTAAT

CTGGTTGTGTGTGTAAAAACATATGGTTAATCTGGTTAAGTCTGGTTAATCATATTAGGTAAGAAAAATG

TAAAGAATGTGTAAGACGAAATTTTTGTAAAGTACTCTGCAAAGCACTTTCACATTTCTGCTTATCAACT

AAACCTCACAGAGATAGTTTAATAGTTTAGGCTTTAAAATGGATTTTGATTATTCAACAAGTGGCCTTCA

TAATTTCTTTAAGTGTTTTTCTTTAAGTATATACTTTCTTTAAATATTTTTTAAAATTTCCTTTTCTCTA

GTAAAGCCAGACCATCCATGCTACCTCTCTAGTGGCACTCTGAAATAAAAAGAAAATAGTTTTCTCTGTT

ATAATTGTATTTGTAATAAGCAGATGAATCACATTTCTTAAAATTTGTTTTAGAGAGGGTAAGCTCTGAC

TAGGACCATGACTTCAATGTGAAATATGTATATATCCTCCGAATCTTTACATATTAAGAATGTATATAGT

CAACTGGTTAAACAGGAAAATCTGGAACCAGCCTGGCTGGGTTTTAATCTTAGCACCATCCTACTAAATG

TTAAATAATATTATAATCTAATGAATAAATGACAATGCAATTCCAAATAGAGTTCATCTGATGACTTCTA

GACTCACAAAATTGCAAGAGAGCTCAGTTGTTGCTCAGTTGTTCCAAATCATGTCGTTTGTTAATTTGTA

ATTAAGCTCCAAAGGATGTATAGCTACTGACAAAAAAAAAAATGAGAATGTAGTTAATCCAAATCAAAAC

TTTCCTATTGCAATGCGTATTTTCTGCTTCATTATCCTTTAATATAATATTTTAAGTTAGCAAGTAATTT

TAATTACAATGCACAAGCCTTGAGAATTATTTTAAATATAAGAAAATCATAATGTTTGATAAAGAAATCA

TGTAAGAAATTTCAAGATAATGGTTTAACAAATAATTTTGTTGATAGAAGATAAGACTAAAAGTGAAATT

CGAAGTGGAGAGGACACTTAAACTGTAGTACTTGTTATGTGTGATTCCAGTAAAAATAGTAATGAGCACT

TATTATTGCCAAGTACTGTTCTGAGGGTACCATATGCAATAAGTTATTTAATCCTTACAATAATCTTGTA

AGGCAGATTCAAACTATCATTACACTTATTTTACAGATGAGAAAACTGGGGCACAGATAAAGCAACTTGC

CCAAGGTCTCATAGCTGTAAGTCAACCCTACGGTCAAGACCTACAAGTAGCCGAGCTCCAGAGTACATTA

TGAGGGTCAAAGATTGTCTTATTACAAATAAATTCCAAGTAGAATCAACCTTTAATAAGTCTTTAATGTC

TCTTAAATATGTTTATATAGGAGTCTAATCACCAATTCACAAAAATGAAAGTAGGGAAATGATTAACAAT

AATCATAGGAATCTAACAATCCAAGTGGCTTGAGAATATTCATTCTTCTTGACAGTATAGATTCTTTACA

ATTTCGTAAGTTCCAATGTATGTTTTAGGAATATGAGGTCATTACTATTCATAATCTGATACAGCTTTAT

CCTAAGGCCTCTCTTTAAAAACTACACTGCATCATAGCTTTTTTGTGCAGTTGGTCTTTCTACTGTTACT

GAACAGTAAGCAACCTACAGATTCACTATCACCAACCAGCCAGTTGATGGATCTTAAGCAAATTATCAAG

CTTGTGATAACCTAAATTATAAAATGAGGGTGTTGGAATAGTTACATTCCAAATCTTCTATAACACTCTG

TATTATATTTCTGCCTCATTCCTTGTAGGGTTTCTTCAGTGCCCGTGGTCATCGACCCCTTGACAAGAAG

AGAGAAGAGGCTCCCAGCCTGAGGCCTGCCCCACCGCCCATCAGTGGAGGTGGCTATCGGGCTCGTCCAG

CCAAAGCAGCTGCCACTCAAAAGAAAGTAGAAAGAAAAGCCCCTGATGCTGGAGGCTGTCTTCACGCTGA

7. Motif

Pfam (5 motifs)

Pfam	Position(Independent E-value)	Description
Fibrinogen_C	238..486(3.8e-95)	PF00147, Fibrinogen beta and gamma chains, C-terminal globular domain
Fib_alpha	91..234(2.2e-48)	PF08702, Fibrinogen alpha/beta chain family
CALCOCO1	113..218(0.19)	PF07888, Calcium binding and coiled-coil domain (CALCOCO1) like
MitMem_reg	158..215(0.39)	PF13012, Maintenance of mitochondrial structure and function
SF-assemblin	157..225(0.37)	PF06705, SF-assemblin/beta giardin

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 (-11771.56) 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 569 positions in the final dataset.

9. SNP

SNP	COORDINATE	AMINO ACID CHANGE	GENE ID	TRANSCRIPT ID	PROTEIN ID	SIFT SCORE	SIFT MEDIAN	SIFT PREDICTION
rs6054	155489608	P265L	ENSG00000171564	ENST00000302068	ENSP00000306099	0.099	2.67	TOLERATED
rs6054	155489608	P46L	ENSG00000171564	ENST00000509493	ENSP00000426757	0.168	2.53	TOLERATED
rs121909621	155490855	L164R	ENSG00000171564	ENST00000509493	ENSP00000426757	0.001	2.61	DELETERIOUS
rs121909621	155490855	L383R	ENSG00000171564	ENST00000302068	ENSP00000306099	0.002	2.75	DELETERIOUS
rs121909622	155491615	G430D	ENSG00000171564	ENST00000302068	ENSP00000306099	0.001	2.67	DELETERIOUS
rs121909622	155491615	G211D	ENSG00000171564	ENST00000509493	ENSP00000426757	0.002	2.57	DELETERIOUS
rs121909624	155488859	L202Q	ENSG00000171564	ENST00000302068	ENSP00000306099	0.024	2.82	DELETERIOUS
rs121909624	155488859		ENSG00000171564	ENST00000509493	ENSP00000426757
rs121909625	155486984	R47*	ENSG00000171564	ENST00000302068	ENSP00000306099

Evolutionary analysis of coding SNPs

SNP	Substitution	Probability of deleterious effect	Pdel
rs6054	P265L	probably damaging	0.74
rs121909621	L383R	possibly damaging	0.5
rs121909622	G430D	probably damaging	0.74
rs121909624	L202Q	possibly damaging	0.5

Provean

SNP Id’s	Amino Acid Change	Probability	Prediction	Score
rs6054	P265L	Deleterious	Damaging	-5.64
rs6054	P46L	Deleterious	Tolerated	-4.03
rs121909621	L164R	Deleterious	Damaging	-3.04
rs121909621	L383R	Deleterious	Damaging	-2.57
rs121909622	G430D	Deleterious	Damaging	-3.5
rs121909622	G211D	Deleterious	Damaging	-3.54
E rs121909624	L202Q	Deleterious	Damaging	-3.14

SNAP2

Wildetype Amino Acid	Position	Variant Amino Acid	Predicted Effect	Score	Expected Accurancy
P	265	L	Effect	96	98%
P	46	L	Neutral	46	78%
L	164	R	Effect	56	98%
L	383	R	Neutral	85	76%
G	430	D	Effect	96	98%
G	211	D	Neutral	86	78%
L	202	Q	Effect	56	98%

Polyphen 2

Rs_Id	Mutation Probability	Score
rs6054	Probably damaging	0.999
rs6054	Possibly damaging	1.00
rs121909621	Probably damaging	0.98
rs121909621	Probably damaging	0.999
rs121909622	Possibly damaging	1.00
rs121909622	Probably damaging	0.98
rs121909624	Probably damaging	0.98

Hope Prediction

Rs_Ids	Mutation	Mapping Issues	AA Variant	Function Impact		Score
rs6054	FGB_P265L	Uniprot Residue:A	P265L	Medium	5.23
rs6054	FGB_P46L		P46L	High	10.8
rs121909621	FGB_L164R		L164R	Medium	4.88
rs121909621	FGB_L383R		L383R	Medium	4.56
rs121909622	FGB_G430D	Uniprot Residue:N	G430D	High	5.94
rs121909622	FGB_G211D		G211D	High	10.8
rs121909624	FGB_L202Q		L202Q	High	6.52

10. Active Site

Rank	C-Score	Cluster Size	PDB Hit	Lig Name	Consensus Building Residues
1	0.30	67	1fzbF	PEPTIDE	398,415,427,428,436,437,438,462
2	0.22	35	1lwuE	CA	411,413,415,416,422
3	0.09	13	1re4B	CA	291,293,294,408
4	0.08	17	2j2pB	SC2	252,269,271,273,284,481
5	0.05	11	2j61A	NAG	271,274,284,343,351,481,483
6	0.05	13	2j2pF	SC2	287,289,305,307,320,321
7	0.04	11	2j0gE	BM3	293,294,295,298,408
8	0.02	6	2oyiE	k-mer	390,391,394
9	0.01	2	2j0yC	CA	409,410
10	0.01	2	2j2pC	SC2	252,273

11. Primary Sequence Analysis

Number of amino acids

491

Molecular weight

55928.15

Theoretical pI

8.54

Amino acid composition

Ala (A) 23 4.7%

Arg (R) 28 5.7%

Asn (N) 32 6.5%

Asp (D) 28 5.7%

Cys (C) 12 2.4%

Gln (Q) 26 5.3%

Glu (E) 30 6.1%

Gly (G) 42 8.6%

His (H) 9 1.8%

Ile (I) 16 3.3%

Leu (L) 36 7.3%

Lys (K) 36 7.3%

Met (M) 18 3.7%

Phe (F) 12 2.4%

Pro (P) 23 4.7%

Ser (S) 34 6.9%

Thr (T) 23 4.7%

Trp (W) 14 2.9%

Tyr (Y) 21 4.3%

Val (V) 28 5.7%

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

C₂₄₄₉H₃₇₉₉N₇₀₁O₇₄₄S₃₀

Total number of atoms

7723

Instability index(II)

42.47

Stability

unstable

Aliphatic index(AI)

62.53

GRAVY

-0.758

12. Secondary structure analysis

Alpha helix (Hh) : 197 is 40.12%

310 helix (Gg) : 0 is 0.00%

Pi helix (Ii) : 0 is 0.00%

Beta bridge (Bb) : 0 is 0.00%

Extended strand (Ee) : 70 is 14.26%

Beta turn (Tt) : 0 is 0.00%

Bend region (Ss) : 0 is 0.00%

Random coil (Cc) : 224 is 45.62%

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	28
Asp-N endopeptidase	28
Asp-N endopeptidase + N-terminal Glu	58
BNPS-Skatole	14
CNBr	18
Chymotrypsin-high specificity (C-term to [FYW], not before P)	45
Chymotrypsin-low specificity (C-term to [FYWML], not before P)	105
Clostripain	28
Formic acid	28
Glutamylendopeptidase	30
Iodosobenzoic acid	14
Hydroxylamine	3
LysC	36
LysN	36
NTCB (2-nitro-5-thiocyanobenzoic acid)	12
Pepsin (pH1.3)	67
Pepsin (pH>2)	116
Proline-endopeptidase	6
Proteinase K	203
Staphylococcal peptidase I	27
Tobacco etch virus protease	1
Thermolysin	109
Trypsin	58

14. Epitope

Rank	Start position	Sequence	Score	Prediction
1	399	HGTDDGVVWMNWKGSW	0.94	Epitope
2	387	YWGGQYTWDMAKHGTD	0.93	Epitope
3	223	QNRQDGSVDFGRKWDP	0.91	Epitope
4	368	DGGGWWYNRCHAANPN	0.90	Epitope
4	343	MFFSTYDRDNDGWLTS	0.90	Epitope
4	232	FGRKWDPYKQGFGNVA	0.90	Epitope
4	114	SELEKHQLYIDETVNS	0.90	Epitope
5	349	DRDNDGWLTSDPRKQC	0.89	Epitope
6	29	APDAGGCLHADPDLGV	0.88	Epitope
6	259	PGEYWLGNDKISQLTR	0.88	Epitope
6	21	TQKKVERKAPDAGGCL	0.88	Epitope
6	2	APPPISGGGYRARPAK	0.88	Epitope
6	190	ETSEMYLIQPDSSVKP	0.88	Epitope
7	168	TVSCNIPVVSGKECEE	0.87	Epitope
8	159	QMEYCRTPCTVSCNIP	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	3
p-value	< 1.0e-16
Protein – Protein Interaction network

16. MRNA

RNA Base Pairing Probability Plot