A few years ago, I was reporting a story about Prevent, the government’s counter-extremism programme. I interviewed various Muslims from around the UK who had interacted with the programme in one way or another. Many wanted to be anonymous. These were ordinary people, not activists, and for many it felt too risky to draw attention to themselves, even if they had not been accused of wrongdoing. “We’re already seen as terrorists,” one young woman told me. “Just look at the way people talk about our community.”

I thought about that young woman as it was announced that Boris Johnson would replace a promised inquiry into allegations of Islamophobia within the Conservatives with a more broad-brush review of how the party handles discrimination complaints. There is compelling evidence that the Conservative party has a specific problem with Islamophobia. During the election campaign, the party continued to back several candidates who had made Islamophobic statements; a dossier of social media comments found that 25 Tory councillors had posted racist material including descriptions of Muslims as “barbarian” and “the enemy within”. The prime minister himself has ridiculed burqa-wearing women as looking like “letterboxes”. A poll in June conducted by YouGov for the anti-racist organisation Hope Not Hate found that more than half of Conservative party members believe that Islam threatens “the British way of life”.

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Beyond the diluted focus of the investigation, the choice of chair suggests something other than the “zero tolerance” of anti-Muslim prejudice that Johnson has promised. Swaran Singh has previously written that “the racism charge” forced politicians to “act before they have had time to think”. He has also contributed to Spiked, an online publication whose editor, Brendan O’Neill, has dismissed Islamophobia as an “invented term” designed to “chill open discussion about aspects of Islam”.

Of course, Singh does not necessarily share O’Neill’s views, but it is worth noting that this is often the terrain on which discussion of Islamophobia takes place – as an issue primarily of semantics, about whether Islam is a religion or a race, a question of free speech and “legitimate criticism” of a religion or an “ideology”. Questioning the very concept of Islamophobia has become another weapon in the rightwing culture war. Just last week Melanie Phillips wrote a column for the Jewish Chronicle; the headline on the website, complete with scare quotes: “Don’t fall for bogus claims of ‘Islamophobia’”. This is a simple but effective deflection from the profoundly serious consequences of systematic discrimination.

Since 2013, the number of reported hate crimes has doubled in the UK; around half of all incidents of religious hatred relate to Muslims. But Islamophobia is more than hate crimes or racist rhetoric. Structural racism means a closing down of opportunity. It means limited space in the public sphere. It means disenfranchisement and underemployment and unequal treatment. Certainly, there have been some breakthroughs in terms of British Muslims in political office and other areas of public life – Sadiq Khan as mayor of London, Sayeeda Warsi as Conservative party co-chair (a post she held from 2010-12). Yet this remains the exception rather than the rule.

A 2017 report by the Social Mobility Commission found that Muslims living in the UK “are being held back from reaching their full potential at every stage of their lives”. The research found that young people from Pakistani and Bangladeshi backgrounds (the largest British Muslim communities) are more likely to succeed in education and go to university than some other groups, but that this does not translate into the labour market.

Within the economically active population (16 to 74 years), only one in five of the Muslim population is in full-time work, compared with more than one in three for the overall population in England and Wales. It also found that nearly half of the Muslim population – 46%– live in the most deprived local authority districts. This socioeconomic and class disadvantage has serious implications for access to resources, attainment, and the availability of jobs. Coupled with more direct racial discrimination – such as stereotyping by teachers and employers, and the fact that people with names that sound “foreign” are less likely to get job interviews – this is a toxic mix.

I have reported on numerous stories that involve British Muslims. I have consistently noticed that political rhetoric has an impact on people’s perception of their own ability to participate in the public sphere.

The disastrous mishandling of Birmingham’s “Trojan horse” affair – in which schools in primarily Muslim areas were accused of fomenting extremism – led to many parents and other local people retreating from governing bodies. This went far beyond the handful of individuals accused of wrongdoing. Several people I interviewed, not just in Birmingham but elsewhere in the country, cited the incident as a reason not to get involved in local politics or services at all. “Whatever we do we are referred to as a national security threat, so why bother?” one Muslim parent told me.

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From these conversations, the impact of a media and political culture that routinely demonises Muslims is clear: people step back, they don’t get involved, they keep their heads down. The end result is that they do not have equal access to public debate and political participation. This is not to say that there are no Muslim individuals or organisations speaking up for their communities, but for many people, it is easier to absorb the message society is sending you and withdraw. The real “chilling effect” of Islamophobia is not on criticism of a set of religious beliefs, but on the democratic participation of a subset of British citizens.

That is why the handling of allegations of endemic Islamophobia within the Conservative party has implications far beyond its internal complaints procedures. If the governing party cannot acknowledge or deal with allegations of institutional racism against a specific group within its own ranks, not only does that send a poor message, it does not bode well for its interest in tackling the problem in the country at large.

• Samira Shackle is deputy editor of the New Humanist and a regular contributor to the Guardian long read