Hi

A gene that contains a lot of GC sequence is more suceptible mutated (hot point mutation)

a bigest gene is more suceptible  mutated by unequal crossing over

a gene which encodes an important physiological function is a abrit from mutation as a gene encoding a function that is not very important.

The characteristics of the sequence is also important, as repetitive DNA regions tend to show higher mutation rates. The genome partition can also interfere, as mitochondrial sequences tend to show higher mutation rates, because of the more oxidative environment, as well as a less effective DNA repair system. As mentioned above, the natural selection regime can be very important too, because regions under strong purifying selection might have lower mutation rates, and regions under balancing selection and neutrality might have higher rates.

Hope this can be helpful.

The rate of sequence mutation can also depend on the the rate of

germline replication, which is higher in rodents than in mammals. 

I think we need to distinguish between mutation and substitution, substitutions being mutations that are passed on to subsequent generations.  Mutations happen essentially randomly (factors such as CpG notwithstanding), whereas selection and drift play a role in determining whether a given mutation is passed on to subsequent generations.  It appears that Abhishek is referring to substitutions and not mutations, since he mentions gene function and protein structure, whereas all the answers only mention the term mutation(s).  Manolo says "regions under strong purifying selection might have lower mutation rates."  I think he meant to refer to "substitutions" rather than mutations, because selection can only act on a change after it has already occurred (mutation has happened).

The following publications may not address all the points Abhishek raises, but I believe they may serve to answer some.  These are two papers that Subramanian and  Kumar published in 2006 (you might want to check other papers by Kumar as well):

1. Higher Intensity of Purifying Selection on >90% of the Human Genes Revealed by the Intrinsic Replacement Mutation Rates. Mol. Biol. Evol., 23(12):2283–2287

2. Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome. BMC Genomics, 7:306 

Hope this helps.

For protein, there is a good review about this topic: determinants of the rate of

protein sequence evolution. Published in nature rev genetics this year. This is an interesting topic.

See a discussion of this subject here:

Annu Rev Microbiol. 2003;57:467-85.

Natural selection and the emergence of a mutation phenotype: an update of the evolutionary synthesis considering mechanisms that affect genome variation.

I realise your questions is more specific in terms of the rate of molecular change in relation to its content, role, location, structure etc. However, in an organismal and phylogenetic context, Bromham's 2009 review identifies body size, reproductive rate, ecology, geographical location and population dynamics as covarying with substitution rate. Maybe there are hints in that which could lead to a better understanding of specifics?

http://rsbl.royalsocietypublishing.org/content/early/2009/04/03/rsbl.2009.0136.short